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Added documentation for statgen

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arcan1s
2013-07-27 23:38:42 +04:00
parent f2ec8c6580
commit 1af86034e7
54 changed files with 3953 additions and 308 deletions
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5
statgen/CMakeLists.txt
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@ -1,7 +1,8 @@
cmake_minimum_required (VERSION 2.8)
cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0003 OLD)
cmake_policy(SET CMP0011 NEW)
cmake_policy(SET CMP0015 NEW)
# set project name
set (PROJECT statgen)
@ -28,4 +29,4 @@ set (LIBRARIES)
set (TARGETS "")
set (HEADERS "")
add_subdirectory (src)
add_subdirectory (${${PROJECT}_SOURCE_DIR})

61
statgen/about.dox Normal file
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@ -0,0 +1,61 @@
/*! @mainpage statgen
*
* @section intro_sec Introduction
*
* <b>Developer</b>:
* <ul>
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
*</ul>
* <b>License</b>:
* <ul>
* <li>GPL
* </ul>
*
* @section How-To-Use How to use
* Usage:
* <pre>
* statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]
* [ -l LOGFILE ] [ -q ] [ -h ]
*
* Parametrs:
* -i - mask of input files
* -s - trajectory steps (integer)
* -c - cell size (float), A
* -a - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc
* -r - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0-interaction
* (<2.4 A) and 0-1 (<3.0) are needed. This flag can be used multiple times
* -o - output file name
* -g - check graph isomorphism. DEPTH is max depth for check cycles (>= 3)
* -l - log enable
* -q - quiet enable
* -h - show this help and exit
* </pre>
*
* @page Install
*
* @section Requirements Requirements
* The application statgen requires the following external stuff:
* - cmake >= 2.8
* - gcc >= 4.8
*
* @section How-To How to install
*
* @subsection Linux Linux
* @code
* mkdir build && cd build
* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
* make
* make install
* @endcode
*
* @subsection Windows Windows
* @code
* create project file using 'cmake'
* compile project
* @endcode
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* * initial release
*/

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51
statgen/src/CMakeLists.txt
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@ -3,62 +3,27 @@ set ("${PROJECT}_VERSION_MINOR" 0)
set ("${PROJECT}_VERSION_PATCH" 1)
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
message (STATUS ${${PROJECT}_VERSION})
message (STATUS "${PROJECT}: Version ${${PROJECT}_VERSION}")
## set files
# main files
set (MAIN_SOURCES main)
# not public srcs
set (PRIVATE_CLASSES)
# headers only files
SET (HEADERS_ONLY)
# public srcs
set (PUBLIC_CLASSES add_main
coords
graph
int2char
messages
stat_print
stat_select
stat_sort
summary_stat)
# public headers
set (PUBLIC_HEADERS)
# shared libraries
# set files
aux_source_directory (. SOURCES)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif()
set (SOURCES)
# append list
foreach (class ${PRIVATE_CLASSES})
LIST (APPEND SOURCES ${class}.c)
LIST (APPEND HEADERS ${class}.h)
endforeach ()
foreach (class ${HEADERS_ONLY})
LIST (APPEND HEADERS ${class}.h)
endforeach ()
foreach (class ${PUBLIC_CLASSES})
LIST (APPEND SOURCES ${class}.c)
LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
endforeach ()
# message
message (STATUS "SOURCES: ${SOURCES}")
# link libraries and compile
add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
add_executable (${PROJECT} ${SOURCES})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
INSTALL (TARGETS ${PROJECT}
DESTINATION bin)
INSTALL (TARGETS ${PROJECT} DESTINATION bin)
if (ADD_INCLUDE)
INSTALL (FILES ${PUBLIC_HEADERS}
DESTINATION include/${PROJECT})
INSTALL (FILES ${PUBLIC_HEADERS} DESTINATION include/${PROJECT})
endif ()

100
statgen/src/add_main.c
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@ -1,14 +1,43 @@
/* Additional library for main.c (statgen)
/**
* @file
*/
#include <stdio.h>
// #include "messages.h"
#include "messages.h"
/**
* @fn error_checking
*/
int error_checking (const float *cell, const int from, const char *input,
const int max_depth, const int num_of_inter, const char *output,
const int to, const int type_inter)
/**
* @brief function that checks errors in input variables
* @code
* error_checking (cell, from, input, max_depth, num_of_inter, output, to,
* type_inter);
* @endcode
*
* @param cell massive of cell size
* @param from first trajectory step
* @param input mask of trajectory files
* @param max_depth max depth for check cycles in graph analyze
* @param num_of_inter number of different interactions
* @param output output file name
* @param to last trajectory step
* @param type_inter number of atoms for interactions
*
* @return 11 - error in 'type_inter'
* @return 12 - error in 'cell'
* @return 13 - error in 'to' or 'from'
* @return 14 - error in 'num_of_inter'
* @return 15 - error in 'input'
* @return 16 - error in 'output'
* @return 19 - error in 'max_depth'
* @return 0 - exit without errors
*/
{
if ((type_inter == 0) || (type_inter > 4))
return 11;
@ -29,10 +58,35 @@ int error_checking (const float *cell, const int from, const char *input,
}
/**
* @fn printing_head
*/
int printing_head (const char *output, const int log, const int quiet,
const char *input, const int from, const int to, const float *cell,
const int type_inter, const int *label_atom,
const int num_of_inter, const float *crit, const int max_depth)
/**
* @brief function that prints header in output file
* @code
* printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
* num_of_inter, crit, max_depth);
* @endcode
*
* @param output output file nams
* @param log status of log-mode
* @param quiet status of quiet-mode
* @param input mask of trajectory files
* @param from first trajectory step
* @param to last trajectory step
* @param cell massive of cell size
* @param type_inter number of atoms for interactions
* @param label_atom massive of atom types for interactions
* @param num_of_inter number of different interactions
* @param crit massive of criteria
* @param max_depth maximum depth for check cycles in graph analyze
*
* @return 0 - exit without errors
*/
{
int i, j;
FILE *f_out;
@ -65,9 +119,26 @@ int printing_head (const char *output, const int log, const int quiet,
return 0;
}
/**
* @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
*/
{
if ((quiet != 1) && (std_output != stderr))
message (0, mode, str, std_output);
@ -78,8 +149,31 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
}
/**
* @fn set_defaults
*/
int set_defaults (float *cell, int *from, char *input, int *log, int *max_depth,
int *num_of_inter, char *output, int *to, int *type_inter, int *quiet)
/**
* @brief function for set default values of variables
* @code
* set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
* &type_inter, &quiet);
* @endcode
*
* @param cell massive of cell size
* @param from first trajectory step
* @param input mask of trajectory files
* @param log status of log-mode
* @param max_depth maximum depth for check cycles in graph analyze
* @param num_of_inter number of different interactions
* @param output output file name
* @param to last trajectory step
* @param type_inter number of atoms for interactions
* @param quiet status of quiet-mode
*
* @return 0 - exit without errors
*/
{
int i;

17
statgen/include/statgen/add_main.h → statgen/src/add_main.h
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@ -1,6 +1,23 @@
/**
* @file
*/
#ifndef ADD_MAIN_H
#define ADD_MAIN_H
/**
* @fn error_checking
*/
/**
* @fn printing_head
*/
/**
* @fn print_message
*/
/**
* @fn set_defaults
*/
int error_checking (const float *, const int, const char *, const int, const int,
const char *, const int, const int);
int printing_head (const char *, const int, const int, const char *, const int,

134
statgen/src/coords.c
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@ -1,50 +1,68 @@
/* Library for reading coordinates from input file
*
* Usage:
* reading_coords (mode, filename, type_interaction, labels,
* cell, &number_of_molecules, &number_of_atoms, true_label_molecule,
* label_molecule, type_atoms, coords, char_type_atoms)
/**
* @file
*/
#include <stdio.h>
#include <stdlib.h>
/**
* @fn reading_coords
*/
int reading_coords (const int mode, const char *filename, const int type_inter,
const int *label_atom, const float *cell, int *num_mol,
int *num_atoms, int *true_label_mol, int *label_mol,
int *type_atoms, float *coords, char *ch_type_atoms)
/* filename - name of file with coordinates
* type_inter - type interaction (number of molecules for interaction)
* label_atom - types of atom for interaction
* cell - cell dimension
* num_mol - number of molecules for writing coordinates
* num_atoms - number of atoms for writing coordinates
* true_label_mol - massive of true numbers of molecule for atoms
* label_mol - massive of numbers of molecule for atoms
* type_atoms - massive of atom types for atoms
* coords - massive of coordinates
* ch_type_atoms - massive of char types for atoms
/**
* @brief function that reads coordinates from special file format
* @code
* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol,
* &num_atoms, true_label_mol, label_mol, type_atoms,
* coords, ch_type_atoms);
* @endcode
*
* @param mode mode of reading; '1' is statgen, '2' is envir or
* frad, '3' is agl
* @param filename input file name
* @param type_inter number of needed atoms
* (number of needed molecules)
* @param label_atom massive of needed atom types
* (massive of needed molecules)
* @param cell massive of cell size
* @param num_mol number of molecules
* @param num_atoms number of atoms
* @param true_label_mol massive of true numbers of molecule for atoms
* @param label_mol massive of numbers of molecule for atoms
* @param type_atoms massive of atom types
* @param coords massive of coordinates
* @param ch_type_atoms massive of char atom types
*
* @return 1 - file $filename does not exist
* @return 2 - unknown mode
* @return 0 - exit without errors
*/
{
char at_symb[32], file_string[256];
int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
float cur_coords[3], *not_tr_coords, ref[3];
FILE *inp;
/* cur_*, at_symb - temp variables
* file_string - temp string variable
* atoms - total number of atoms in system
* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
* ref_mol - number of molecule for reference
* not_tr_coords - not translated coordinates
* ref - coordinates of reference molecule
* inp - file with input data
/* cur_* temp variables
* at_symb temp variable
* file_string temp string variable
* atoms total number of atoms in system
* tr_num_atoms number of translated atoms (must be 8*num_atoms)
* ref_mol number of molecule for reference in translation
* not_tr_coords massive of not translated coordinates
* ref massive of coordinates of reference molecule
* inp input file
*/
/// <b>Work blocks</b>
*num_atoms = 0;
*num_mol = 0;
// Reading file
/// <pre> reading file </pre>
inp = fopen (filename, "r");
if (inp == NULL)
return 1;
@ -59,10 +77,11 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
// reading variables according to selected mode
switch (mode)
{
case 0:
// for statgen
// mode == 0 (selected atoms)
for (j=0; j<type_inter; j++)
if (cur_at_type == label_atom[j])
{
@ -83,7 +102,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
break;
case 1:
// for envir
// mode == 1 (all atoms)
not_tr_coords[3**num_atoms+0] = cur_coords[0];
not_tr_coords[3**num_atoms+1] = cur_coords[1];
not_tr_coords[3**num_atoms+2] = cur_coords[2];
@ -101,18 +120,41 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
*num_atoms = *num_atoms + 1;
break;
default: return 1;
case 2:
// mode == 2 (selected molecules)
for (j=0; j<type_inter; j++)
if (cur_mol == label_atom[j])
{
not_tr_coords[3**num_atoms+0] = cur_coords[0];
not_tr_coords[3**num_atoms+1] = cur_coords[1];
not_tr_coords[3**num_atoms+2] = cur_coords[2];
ch_type_atoms[2**num_atoms+0] = at_symb[0];
ch_type_atoms[2**num_atoms+1] = at_symb[1];
if (ref_mol != cur_mol)
{
ref_mol = cur_mol;
true_label_mol[*num_mol] = ref_mol;
*num_mol = *num_mol + 1;
}
label_mol[*num_atoms] = *num_mol - 1;
type_atoms[*num_atoms] = j;
*num_atoms = *num_atoms + 1;
}
break;
default: return 2;
}
}
fclose (inp);
// Translation
/// <pre> translation </pre>
tr_num_atoms = *num_atoms;
for (i=0; i<*num_atoms; i++)
for (j=0; j<3; j++)
coords[3*i+j] = not_tr_coords[3*i+j];
// Assign initial value to reference coordinates
// assign initial value to reference coordinates
ref_mol = label_mol[0];
for (i=0; i<3; i++)
ref[i] = coords[3*0+i];
@ -129,7 +171,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
for (x=0; x<3; x++)
{
if (ref[x] >= 0.0)
// if xyz >= 0.0 A
// if xyz >= 0.0 A
{
for (j=0; j<3; j++)
if (j == x)
@ -142,7 +184,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
tr_num_atoms++;
}
else
// if xyz < 0.0 A
// if xyz < 0.0 A
{
for (j=0; j<3; j++)
if (j == x)
@ -161,7 +203,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
for (y=x+1; y<3; y++)
{
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
// if xyz and xyz >= 0.0 A
// if xyz and xyz >= 0.0 A
{
for (j=0; j<3; j++)
if ((j == x) || (j == y))
@ -175,7 +217,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[x] < 0.0) && (ref[y] < 0.0))
// if xyz and xyz < 0.0 A
// if xyz and xyz < 0.0 A
{
for (j=0; j<3; j++)
if ((j == x) || (j == y))
@ -191,7 +233,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
for (y=0; y<3; y++)
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
// if xyz OR xyz >= 0.0
// if xyz OR xyz >= 0.0
{
for (j=0; j<3; j++)
{
@ -210,7 +252,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
// if x and y and z >= 0.0 A
// if x and y and z >= 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -222,7 +264,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
// if x and y >= 0.0 A and z < 0.0 A
// if x and y >= 0.0 A and z < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -234,7 +276,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
// if x and z >= 0.0 A and y < 0.0 A
// if x and z >= 0.0 A and y < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -246,7 +288,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
// if y and z >= 0.0 A and x < 0.0 A
// if y and z >= 0.0 A and x < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -258,7 +300,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
// if x and y < 0.0 A and z >= 0.0 A
// if x and y < 0.0 A and z >= 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -270,7 +312,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
// if x and z < 0.0 A and y >= 0.0 A
// if x and z < 0.0 A and y >= 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
@ -282,7 +324,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
// if x >= 0.0 A and y and z < 0.0 A
// if x >= 0.0 A and y and z < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -294,7 +336,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
// if x and y and z < 0.0 A
// if x and y and z < 0.0 A
{
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
@ -306,7 +348,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
}
}
// free memory
/// <pre> free memory </pre>
free (not_tr_coords);
return 0;

8
statgen/include/statgen/coords.h → statgen/src/coords.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef COORDS_H
#define COORDS_H
/**
* @fn reading_coords
*/
int reading_coords (const int, const char *, const int, const int *,
const float *, int *, int *, int *, int *, int *, float *,
char *);

106
statgen/src/graph.c
View File

@ -1,46 +1,77 @@
/* Library for graph structure analyze
* Usage:
* graph_analyze (N, connect, max_depth, isomorphism_class)
/**
* @file
*/
#include <math.h>
#include <stdlib.h>
/**
* @fn check_cycle
*/
int check_cycle (const int N, const int *pn)
// function to return number of cycles
/**
* @brief function that calculates number of cycles in graph
* @code
* cycle = check_cycle (N, pn);
* @endcode
*
* @param N number of vertexes
* @param pn massive of number of vertexes with weight equals to i
*
* @return number of cycles
*/
{
int cycle, i;
/* cycle - number of cycle
/* cycle number of cycle
*/
cycle = 0;
for (i=1; i<N; i++)
cycle += i*pn[i];
// for linear (0.5*cycle == N-1)
// for linear (0.5*cycle == N-1)
cycle = 0.5 * cycle - (N - 1);
return cycle;
}
/**
* @fn check_cycle_size
*/
int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cycle)
// function to return number of cycles of certain size
/**
* @brief function that returns number of cycles different size
* @code
* check_cycle_size (N, matrix, depth, n_cycle);
* @endcode
*
* @param N number of vertexes
* @param matrix connectivity matrix
* @param depth depth of search (maximum number of vertexes in cycle)
* @param n_cycle massive of number of cycle with number of vertexes
* equals to i
*
* @return 1 - memory error
* @return 0 - exit without errors
*/
{
int cur_N, cycle, i, j, k, n, p, *vertex;
/* cur_N - current number of elements in submatrix
* cycle - if (cycle == 1) that cycle exist
* n - number of samples
* vertex - vertexes of subgraph
/* cur_N current number of elements in submatrix
* cycle if (cycle == 1) that cycle exist
* n number of samples
* vertex vertexes of subgraph
*/
vertex = (int *) malloc (N * sizeof (int));
if (vertex == NULL)
return 1;
for (i=0; i<depth-2; i++)
n_cycle[i] = 0;
// matrix generation from
// http://wincode.org/acm-icpc/subsets-generation
// matrix generation from
// http://wincode.org/acm-icpc/subsets-generation
n = pow (2, N);
for (i=0; i<n; i++)
{
@ -54,7 +85,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
if ((cur_N > 2) && (cur_N <= depth))
{
// copy connectivity matrix
// copy connectivity matrix
cycle = 1;
for (j=0; j<cur_N; j++)
{
@ -65,7 +96,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
cycle = 0;
}
// analyze subgraph
// analyze subgraph
if (cycle == 1)
n_cycle[cur_N-3]++;
}
@ -77,32 +108,56 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
}
/**
* @fn check_tail
*/
int check_tail (const int *pn)
// function to return number of tails
/**
* @brief function that calculates number of tails
* @code
* tails = check_tail (pn);
* @endcode
*
* @param pn massive of number of vertexes with weight equals to i
*
* @return number of tails
*/
{
return pn[1];
}
/**
* @fn graph_analyze
*/
int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso)
/* N - number of vertex in graph
* matrix - connectivity matrix
* max_depth - maximum depth for check_cycle_size
* iso - isomorphism class
/**
* @brief function that analyzes graph isomorhic class
* @code
* graph_analyze (N, matrix, max_depth, iso);
* @endcode
*
* @param N number of vertexes
* @param matrix connectivity matrix
* @param max_depth maximum depth of search for check_cycle_size
* @param iso isomorphism class
*
* @return 1 - memory error
* @return 0 - exit without errors
*/
{
int depth, i, j, *n_cycle, p, *pn;
/* depth - depth for check_cycle_size
* n_cycle - number of cycle
* p - current weight
* pn - total weight
/* depth depth of search for check_cycle_size
* n_cycle number of cycle
* p current weight
* pn massive of number of vertexes with weight equals to i
*/
if (max_depth > N)
depth = N;
else
depth = max_depth;
// convert to matrix of weight
// convert to matrix of weight
pn = (int *) malloc (N * sizeof (int));
n_cycle = (int *) malloc ((depth - 2) * sizeof (int));
if ((pn == NULL) ||
@ -129,6 +184,7 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
iso[i+2] = n_cycle[i];
}
// free memory
free (n_cycle);
free (pn);

17
statgen/include/statgen/graph.h → statgen/src/graph.h
View File

@ -1,6 +1,23 @@
/**
* @file
*/
#ifndef GRAPH_H
#define GRAPH_H
/**
* @fn graph_analyze
*/
/**
* @fn check_cycle
*/
/**
* @fn check_cycle_size
*/
/**
* @fn check_tail
*/
int graph_analyze (const int, const int *, const int, int *);
int check_cycle (const int, const int *);
int check_cycle_size (const int, const int *, const int, int *);

20
statgen/src/int2char.c
View File

@ -1,12 +1,22 @@
/* Library for converting integer to string
* Usage
* char = conv (number, position)
/**
* @file
*/
/**
* @fn conv
*/
char conv (const int fnumb, const int dig_pos)
/* fnumb - integer
* dig_pos - position
/**
* @brief function that converts from integer to char
* @code
* char = conv (N, 0);
* @endcode
*
* @param fnumb integer
* @param dig_pos position: ones=1, decimals=2, hundreds=3
*
* @return char
*/
{
int d, h, o;

8
statgen/include/statgen/int2char.h → statgen/src/int2char.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef INT2CHAR_H
#define INT2CHAR_H
/**
* @fn conv
*/
char conv (const int, const int);
#endif /* INT2CHAR_H */

122
statgen/src/main.c
View File

@ -1,17 +1,21 @@
/**
* @file
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
// #include "add_main.h"
// #include "coords.h"
// #include "int2char.h"
// #include "messages.h"
// #include "stat_print.h"
// #include "stat_select.h"
// #include "stat_sort.h"
// #include "summary_stat.h"
#include "add_main.h"
#include "coords.h"
#include "int2char.h"
#include "messages.h"
#include "stat_print.h"
#include "stat_select.h"
#include "stat_sort.h"
#include "summary_stat.h"
int main (int argc, char *argv[])
@ -26,40 +30,40 @@ int main (int argc, char *argv[])
int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms,
num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to,
*true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
/* input - mask of input files
* logfile - log file name
* output - output file name
/* input mask of trajectory files
* logfile log file name
* output output file name
*
* cell - cell dimension
* coords - massive of coordinates
* crit - massive of criteria
* cell massive of cell size
* coords massive of coordinates
* crit massive of criteria
*
* agl - massive of aglomerates
* connect - connectivity graph for all molecules
* from - start point
* label_atom - types of atom for interaction
* label_mol - massive of numbers of molecule for atoms
* log - status of log-mode
* max_depth - max depth for check cycles in graph analyze
* num_atoms - number of atoms for writing coordinates
* num_mol - number of molecules for writing coordinates
* num_mol_agl - massive of numbers of molecule in aglomerates
* num_of_inter - number of different interactions
* stat - massive of statistics
* stat_all - massive of summary statistics
* step - $(to - from + 1)
* to - finish point
* true_label_mol - massive of true numbers of molecule for atoms
* type_agl - massive of numbers of aglomerate types
* type_atoms - massive of atom types for atoms
* type_inter - type interaction (number of molecules for interaction)
* quiet - status of quiet-mode
* agl massive of aglomerates
* connect connectivity graph for all molecules
* from first trajectory step
* label_atom massive of atom types for interactions
* label_mol massive of numbers of molecule for atoms
* log status of log-mode
* max_depth maximum depth for check cycles in graph analyze
* num_atoms number of atoms
* num_mol number of molecules
* num_mol_agl massive of number of molecules in aglomerates
* num_of_inter number of different interactions
* stat massive of statistic
* stat_all massive of summary statistic
* step $(to - from + 1)
* to last trajectory step
* true_label_mol massive of true numbers of molecule for atoms
* type_agl massive of number of aglomerate types
* type_atoms massive of atom types
* type_inter number of atoms for interactions
* quiet status of quiet-mode
*/
set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
&type_inter, &quiet);
// reading number of interactions
// reading number of interactions
for (i=1; i<argc; i++)
if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
num_of_inter++;
@ -71,7 +75,7 @@ int main (int argc, char *argv[])
num_of_inter = 0;
}
// reading arguments
// reading arguments
for (i=1; i<argc; i++)
{
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
@ -99,13 +103,13 @@ int main (int argc, char *argv[])
return 0;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
// mask of input files
// mask of input files
{
strcpy (input, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
// steps
// steps
{
sscanf (argv[i+1], "%i,%i", &from, &to);
if (from > to)
@ -118,13 +122,13 @@ int main (int argc, char *argv[])
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
// cell size
// cell size
{
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
// atom types
// atom types
{
type_inter = 1;
for (j=0; j<strlen(argv[i+1]); j++)
@ -153,7 +157,7 @@ int main (int argc, char *argv[])
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
// criteria
// criteria
{
index = 0;
sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
@ -172,26 +176,26 @@ int main (int argc, char *argv[])
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
// output file
// output file
{
strcpy (output, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'g'))
// graph isomorphism scan
// graph isomorphism scan
{
sscanf (argv[i+1], "%i", &max_depth);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
// log mode
// log mode
{
log = 1;
strcpy (logfile, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
// quiet mode
// quiet mode
{
quiet = 1;
}
@ -203,7 +207,7 @@ int main (int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 0, argv[0]);
print_message (quiet, stdout, log, f_log, 1, argv[0]);
// error checking
// error checking
error = error_checking (cell, from, input, max_depth, num_of_inter, output, to,
type_inter);
if (error != 0)
@ -214,8 +218,8 @@ int main (int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 2, argv[0]);
// processing
// initial variables
// processing
// initial variables
k = strlen (input);
strcpy (filename, input);
filename[k] = '.';
@ -237,13 +241,13 @@ int main (int argc, char *argv[])
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
type_agl = (int *) malloc ((max_depth + 2) * sizeof (int));
type_atoms = (int *) malloc (8 * num_atoms * sizeof (int));
// temporary declaration of variables
// temporary declaration of variables
agl = (int *) malloc (2 * 2 * sizeof (int));
connect = (int *) malloc (2 * 2 * sizeof (int));
num_mol_agl = (int *) malloc (2 * sizeof (int));
stat = (int *) malloc (2 * sizeof (int));
stat_all = (int *) malloc (2 * sizeof (int));
// error checking
// error checking
if ((coords == NULL) ||
(label_mol == NULL) ||
(true_label_mol == NULL) ||
@ -258,7 +262,7 @@ int main (int argc, char *argv[])
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 17;
}
// set type_agl to zero
// set type_agl to zero
for (i=0; i<max_depth+2; i++)
type_agl[i] = 0;
sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n\
@ -280,15 +284,15 @@ int main (int argc, char *argv[])
sprintf (tmp_str, "%s%6cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
print_message (quiet, stdout, log, f_log, 5, tmp_str);
// head
// head
printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
num_of_inter, crit, max_depth);
// main cycle
// main cycle
print_message (quiet, stdout, log, f_log, 6, argv[0]);
for (i=from; i<to+1; i++)
{
// reading coordinates
// reading coordinates
filename[k+1] = conv (i, 3);
filename[k+2] = conv (i, 2);
filename[k+3] = conv (i, 1);
@ -304,7 +308,7 @@ int main (int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 8, tmp_str);
}
// resize dynamic arrays
// resize dynamic arrays
agl = (int *) realloc (agl, num_mol * num_mol * sizeof (int));
connect = (int *) realloc (connect, num_mol * num_mol * sizeof (int));
num_mol_agl = (int *) realloc (num_mol_agl, num_mol * sizeof (int));
@ -315,7 +319,7 @@ int main (int argc, char *argv[])
for (j=0; j<num_mol; j++)
stat_all[j] = 0;
}
// error checking
// error checking
if ((agl == NULL) ||
(connect == NULL) ||
(num_mol_agl == NULL) ||
@ -327,7 +331,7 @@ int main (int argc, char *argv[])
}
print_message (quiet, stdout, log, f_log, 9, argv[0]);
// analyze
// analyze
if (error == 0)
{
error = 1;
@ -352,11 +356,11 @@ int main (int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 13, argv[0]);
print_message (quiet, stdout, log, f_log, 14, output);
// tail
// tail
summary_statistic (output, step, num_mol, max_depth, type_agl, stat_all);
print_message (quiet, stdout, log, f_log, 15, argv[0]);
// free memory
// free memory
free (agl);
free (connect);
free (coords);

24
statgen/src/messages.c
View File

@ -1,16 +1,27 @@
/* Library for printing messages at output
*
* Usage:
* message (log, mode, text, output)
/**
* @file
*/
#include <stdio.h>
#include <time.h>
/**
* @fn message
*/
int message (const int log, const int mode, const char *text, FILE *output)
/* mode - number of message
* text - additional text
/**
* @brief function that prints messages to output
* @code
* message (log, mode, text, output);
* @endcode
*
* @param log equal to 1 if print to logfile
* @param mode number of message
* @param text additional text
* @param output output file (may be stdout)
*
* @return 0 - exit without errors
*/
{
char out[4096];
@ -18,6 +29,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
if (log == 1)
{
char time_str[256];
time_t t = time (NULL);
struct tm* aTm = localtime (&t);
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,

8
statgen/include/statgen/messages.h → statgen/src/messages.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef MESSAGES_H
#define MESSAGES_H
/**
* @fn message
*/
int message (const int, const int, const char *, FILE *);
#endif /* MESSAGES_H */

85
statgen/src/stat_print.c
View File

@ -1,57 +1,69 @@
/* Library for printing aglomerates
*
* Usage:
* printing_agl (input_file, output_file, number_of_molecules,
* true_label_molecules, num_of_molecules_in_aglomerates, aglomerates,
* statistic, max_depth, type_of_aglomerate)
/**
* @file
*/
#include <stdio.h>
#include <stdlib.h>
// #include "graph.h"
#include "graph.h"
/**
* @fn printing_agl
*/
int printing_agl (const char *input, const char *output, const int *connect,
const int num_mol, const int *true_label_mol, const int *num_mol_agl,
const int *agl, const int *stat, const int max_depth, int *type_agl)
/* input - name of file with coordinates
* output - name of output file
* connect - connectivity graph for all molecules
* num_mol - number of molecules
* true_label_mol - massive of true numbers of molecule for atoms
* num_mol_agl - massive of numbers of molecule in aglomerates
* agl - massive of aglomerates
* stat - massive of statistics
* max_depth - max depth for check cycles in graph analyze
* type_agl - massive of numbers of aglomerate types
/**
* @brief function that prints aglomerates to output file
* @code
* printing_agl (input_file, output_file, number_of_molecules,
* true_label_molecules, num_of_molecules_in_aglomerates, aglomerates,
* statistic, max_depth, type_of_aglomerate);
* @endcode
*
* @param input input file name
* @param output output file name
* @param connect connectivity graph for all molecules
* @param num_mol number of molecules
* @param true_label_mol massive of true numbers of molecule for atoms
* @param num_mol_agl massive of number of molecules in aglomerates
* @param agl massive of aglomerates
* @param stat massive of statistic
* @param max_depth maximum depth for check cycles in graph analyze
* @param type_agl massive of number of aglomerate types
*
* @return 1 - memory error
* @return 0 - exit without errors
*/
{
int error, i, *iso, j, k, *label_matrix, *matrix;
FILE *f_out;
/* iso - isomorphic graph in database
* label_matrix - massive of indexes of molecule
* matrix - connectivity graph
* f_out - output file
/* iso isomorphic graph in database
* label_matrix massive of indexes of molecule
* matrix connectivity graph
* f_out output file
*/
/// <b>Work blocks</b>
iso = (int *) malloc (max_depth * sizeof (int));
if (iso == NULL)
return 1;
f_out = fopen (output, "a");
// head
/// <pre> print header </pre>
fprintf (f_out, "FILE=%s\nSTATISTIC\n| n | N |\n-----------------\n", input);
for (i=0; i<num_mol; i++)
if (stat[i] != 0)
fprintf (f_out, " %7i %7i \n", i+1, stat[i]);
fprintf (f_out, "-----------------\n");
// body
/// <pre> print body </pre>
for (i=0; i<num_mol; i++)
if (num_mol_agl[i] > 0)
{
// creating connectivity graph
/// <pre> creating connectivity graph </pre>
label_matrix = (int *) malloc (num_mol * sizeof (int));
matrix = (int *) malloc (num_mol_agl[i] * num_mol_agl[i] * sizeof (int));
if ((matrix == NULL) ||
@ -71,34 +83,34 @@ int printing_agl (const char *input, const char *output, const int *connect,
matrix[label_matrix[agl[num_mol*i+k]]*num_mol_agl[i]+label_matrix[agl[num_mol*i+j]]] = 1;
}
// graph topology analyze
/// <pre> graph topology analyze </pre>
if (max_depth > 0)
error = graph_analyze (num_mol_agl[i], matrix, max_depth, iso);
if (error > 0)
return 1;
// printing class of aglomerate
// print class of aglomerate
fprintf (f_out, "AGL=%i=", num_mol_agl[i]);
for (j=0; j<max_depth; j++)
{
// number of tails
// number of tails
if (j == 0)
if (iso[j] > 2)
// branched
// branched
type_agl[3]++;
else
// not branched
// not branched
type_agl[2]++;
// number of cycles
// number of cycles
else if (j == 1)
if (iso[j] > 0)
// cycle
// cycle
type_agl[1]++;
else
// linear
// linear
type_agl[0]++;
else if (j > 1)
// number of n_cycles
// number of n_cycles
type_agl[j+2] += iso[j];
fprintf (f_out, "%i.", iso[j]);
@ -108,20 +120,21 @@ int printing_agl (const char *input, const char *output, const int *connect,
{
fprintf (f_out, "%7i=", true_label_mol[agl[num_mol*i+j]]);
for (k=0; k<num_mol_agl[i]; k++)
{
if (matrix[j*num_mol_agl[i]+k] == 1)
fprintf (f_out, "%i,", true_label_mol[agl[num_mol*i+k]]);
}
fprintf (f_out, "\n");
}
// free memory
/// <pre> free memory </pre>
free (matrix);
free (label_matrix);
}
fprintf (f_out, "---------------------------------------------------\n");
fclose (f_out);
/// <pre> free memory </pre>
free (iso);
return 0;
}

8
statgen/include/statgen/stat_print.h → statgen/src/stat_print.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef STAT_PRINT_H
#define STAT_PRINT_H
/**
* @fn printing_agl
*/
int printing_agl (const char *, const char *, const int *, const int, const int *,
const int *, const int *, const int *, const int,int *);

56
statgen/src/stat_select.c
View File

@ -1,35 +1,47 @@
/* Library for creating connectivity matrix
*
* Usage:
* create_matrix (number_of_molecules, number_of_atoms, label_molecule,
* type_atoms, coords, number_of_interactions, criteria, connect_matrix)
/**
* @file
*/
#include <math.h>
#include <stdlib.h>
/**
* @fn create_matrix
*/
int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
const int *type_atoms, const float *coords, const int num_of_inter,
const float *crit, int *connect)
/* num_mol - number of molecules
* num_atoms - number of atoms
* label_mol - massive of numbers of molecule for atoms
* type_atoms - massive of atom types for atoms
* coords - massive of coordinates
* num_of_inter - number of different interactions
* crit - massive of criteria
* connect - connectivity graph for all molecules
/**
* @brief function that creates connectivity matrix
* @code
* create_matrix (number_of_molecules, number_of_atoms, label_molecule,
* type_atoms, coords, number_of_interactions, criteria, connect_matrix);
* @endcode
*
* @param num_mol number of molecules
* @param num_atoms number of atoms
* @param label_mol massive of numbers of molecule for atoms
* @param type_atoms massive of atom types
* @param coords massive of coordinates
* @param num_of_inter number of different interactions
* @param crit massive of criteria
* @param connect connectivity graph for all molecules
*
* @return 1 - memory error
* @return 0 - exit without errors
*/
{
float r;
int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
/* r - radius
* cur_num_inter - current number of true interactions
* num_inter - needed number of true interactions
* label_inter - temporary massive of true interactions
/* r radius
* cur_num_inter current number of true interactions
* num_inter needed number of true interactions
* label_inter temporary massive of true interactions
*/
/// <b>Work blocks</b>
label_inter = (int ***) malloc (num_mol * sizeof (int **));
for (i=0; i<num_mol; i++)
{
@ -44,10 +56,10 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
if (label_inter == NULL)
return 1;
// creating initial connectivity matrix
/// <pre> creating initial connectivity matrix </pre>
for (i=0; i<num_atoms*8; i++)
for (j=i+1; j<num_atoms*8; j++)
// if atoms from different molecules
// if atoms from different molecules
if (label_mol[i] != label_mol[j])
{
r = sqrt (pow ((coords[3*i+0]-coords[3*j+0]), 2) +
@ -68,10 +80,10 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
for (j=0; j<num_mol; j++)
connect[i*num_mol+j] = 0;
// processing of initial connectivity matrix
/// <pre> processing of initial connectivity matrix </pre>
for (k=0; k<num_of_inter; k++)
{
// determination of the number of interactions
// determination of the number of interactions
num_inter = 0;
for (l=0; l<16; l++)
if (crit[16*k+l] != 0.0)
@ -92,7 +104,7 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
}
}
// free memory
/// <pre> free memory</pre>
for (i=0; i<num_mol; i++)
{
for (j=0; j<num_mol; j++)

8
statgen/include/statgen/stat_select.h → statgen/src/stat_select.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef STAT_SELECT_H
#define STAT_SELECT_H
/**
* @fn create_matrix
*/
int create_matrix (const int, const int, const int *, const int *, const float *,
const int, const float *, int *);

47
statgen/src/stat_sort.c
View File

@ -1,29 +1,41 @@
/* Library for processing connectivity matrix
*
* Usage:
* proc_matrix (number_of_molecules, connect_matrix,
* num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic)
/**
* @file
*/
#include <stdlib.h>
/**
* @fn proc_matrix
*/
int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *agl,
int *stat, int *stat_all)
/* num_mol - number of molecules
* connect - connectivity graph for all molecules
* num_mol_agl - massive of numbers of molecule in aglomerates
* agl - massive of aglomerates
* stat - massive of statistics
* stat_all - massive of summary statistics
/**
* @brief function that processes connectivity matrix
* @code
* proc_matrix (number_of_molecules, connect_matrix,
* num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic);
* @endcode
*
* @param num_mol number of molecules
* @param connect connectivity graph for all molecules
* @param num_mol_agl massive of number of molecules in aglomerates
* @param agl massive of aglomerates
* @param stat massive of statistic
* @param stat_all massive of summary statistic
*
* @return 1 - memory error
* @return 0 - exit without errors
*/
{
int i, j, k, p, *bin;
/* p - weight / graph index
* bin - binary massive of labels
/* p weight / graph index
* bin binary massive of labels
*/
// definition and zeroing
/// <b>Work blocks</b>
// definition and zeroing
bin = (int *) malloc (num_mol * sizeof (int));
if (bin == NULL)
return 1;
@ -36,7 +48,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
agl[num_mol*i+j] = 0;
}
// select non-bonded molecules
/// <pre> select non-bonded molecules </pre>
for (i=0; i<num_mol; i++)
{
p = 0;
@ -50,7 +62,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
}
}
// unwraping of connectivity matrix
/// <pre> unwraping of connectivity matrix </pre>
p = 0;
for (i=0; i<num_mol; i++)
if (bin[i] == 1)
@ -71,7 +83,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
p++;
}
// filling statistic array
/// <pre> filling statistic array </pre>
i = 0;
while (num_mol_agl[i] > 0)
{
@ -80,6 +92,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
i++;
}
/// <pre> free memory </pre>
free (bin);
return 0;

8
statgen/include/statgen/stat_sort.h → statgen/src/stat_sort.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef STAT_SORT_H
#define STAT_SORT_H
/**
* @fn proc_matrix
*/
int proc_matrix (const int, const int *, int *, int *, int *, int *);
#endif /* STAT_SORT_H */

52
statgen/src/summary_stat.c
View File

@ -1,29 +1,39 @@
/* Library for summary statistic
* Usage:
* summary_statistic (filename, number_of_step, number_of_molecules,
* max_depth, type_of_aglomerate, summary_statistic)
/**
* @file
*/
#include <stdio.h>
/**
* @fn summary_statistic
*/
int summary_statistic (const char *filename, const int step, const int num_mol,
const int max_depth, const int *type_agl, const int *stat_all)
/* filename - name of output file
* step - number of steps
* num_mol - number of molecules
* max_depth - max depth for check cycles in graph analyze
* type_agl - massive of numbers of aglomerate types
* stat_all - massive of summary statistics
/**
* @brief function that prints summary statistic
* @code
* summary_statistic (filename, number_of_step, number_of_molecules, max_depth,
* type_of_aglomerate, summary_statistic);
* @endcode
*
* @param filename output file name
* @param step number of steps
* @param num_mol number of molecules
* @param max_depth maximum depth for check cycles in graph analyze
* @param type_agl massive of number of aglomerate types
* @param stat_all massive of summary statistic
*
* @return 0 - exit without errors
*/
{
float conc, p, pn, type[2], x, y;
int i, index;
FILE *f_out;
/* conc - concentrate of aglomerates
* p - probability of aglomerates
* pn - weight probability of aglomerates
* f_out - output file
/* conc concentrate of aglomerates
* p probability of aglomerates
* pn weight probability of aglomerates
* f_out output file
*/
index = 0;
@ -31,19 +41,19 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
if (stat_all[i] != 0)
index = i;
// head
// head
f_out = fopen (filename, "a");
fprintf (f_out, "SUMMARY STATISTIC\n");
fprintf (f_out, "| n | N | C | p | pn |\n------------------------------------------------\n");
for (i=0; i<index+1; i++)
{
// calculating concentrates
// calculating concentrates
x = stat_all[i];
y = step;
conc = x / y;
// calculating probabilityes
// calculating probabilityes
x = (i + 1) * stat_all[i];
y = step * num_mol;
p = x / y;
@ -54,18 +64,18 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
if (max_depth > 0)
{
// types of aglomerates
// types of aglomerates
fprintf (f_out, "------------------------------------------------\n");
// linear and cycle
// linear and cycle
x = type_agl[0] + type_agl[1];
type[0] = type_agl[0];
type[1] = type_agl[1];
fprintf (f_out, "LINEAR=%7.5f\nCYCLE=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
// branched
// branched
type[0] = type_agl[2];
type[1] = type_agl[3];
fprintf (f_out, "NOT BRANCHED=%7.5f\nBRANCHED=%7.5f\n--------------------\n", type[0]/x, type[1]/x);
// n_cycle
// n_cycle
x = 0;
for (i=4; i<max_depth+2; i++)
x += type_agl[i];

8
statgen/include/statgen/summary_stat.h → statgen/src/summary_stat.h
View File

@ -1,6 +1,14 @@
/**
* @file
*/
#ifndef SUMMARY_STAT_H
#define SUMMARY_STAT_H
/**
* @fn summary_statistic
*/
int summary_statistic (const char *, const int, const int, const int, const int *,
const int *);

22
statgen/statgen.cmake
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@ -1,22 +1,32 @@
# set directories
set (${PROJECT}_BINARY_DIR bin)
set (${PROJECT}_SOURCE_DIR src:include)
set (${PROJECT}_SOURCE_DIR src)
set (${PROJECT}_INCLUDE_DIR include)
set (${PROJECT}_LIB_DIR lib)
set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
# include_path
include_directories (${${PROJECT}_INCLUDE_DIR}/${PROJECT}
${${PROJECT}_SOURCE_DIR})
# library path
link_directories (${${PROJECT}_LIB_DIR})
# executable path
set (EXECUTABLE_OUTPUT_PATH ${${PROJECT}_BINARY_DIR})
# verbose
set (CMAKE_VERBOSE_MAKEFILE ON)
# flags
if ( WITH_DEBUG_MODE )
ADD_DEFINITIONS ( -DDEBUG_MODE=1 )
add_definitions ( -DDEBUG_MODE=1 )
endif ()
if ( CMAKE_COMPILER_IS_GNUCXX )
set (ADD_CXX_FLAGS "-Wall")
set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
set (CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
elseif ( MSVC )
set (ADD_CXX_FLAGS "/W4")
set (CMAKE_CXX_FLAGS "${ADD_CXX_FLAGS}")
else ()
message (STATUS "Flags not enabled")
message ("Unknown compiler")
endif ()

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