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arcan1s
2014-01-26 03:49:43 +04:00
parent 473d195ea9
commit 7c874ca96d
170 changed files with 3170 additions and 14746 deletions
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21
mathmech/mm/src/CMakeLists.txt Normal file
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# set files
file (GLOB SOURCES *.c)
file (GLOB HEADERS *.h)
# set library
if (CMAKE_COMPILER_IS_GNUCXX)
set (ADDITIONAL_LIB m)
else ()
set (ADDITIONAL_LIB)
endif ()
# message
message (STATUS "${PROJECT} SOURCES: ${SOURCES}")
message (STATUS "${PROJECT} HEADERS: ${HEADERS}")
# link libraries and compile
add_library (${PROJECT} SHARED ${SOURCES} ${HEADERS})
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
# install properties
install (TARGETS ${PROJECT} DESTINATION lib)

87
mathmech/mm/src/atom_types.c Normal file
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/**
* @file
*/
#include <stdio.h>
/**
* @fn reading_atoms
*/
int reading_atoms (const char *input_at, int *num_types, int *num_mol, int *num_atoms,
char *ch_atom_types, int *atom_types, const int total_types)
/**
* @brief function that reads atom types from input file
* @code
* reading_atoms (input_at, &num_types, num_mol, num_atoms, ch_atom_types, atom_types,
* total_types);
* @endcode
*
* @param input_at input file name with atom types
* @param num_types number of molecule types
* @param num_mol massive of number of molecules of selected type
* @param num_atoms massive of number of atoms of selected molecule
* @param ch_atom_types massive of char atom types
* @param atom_types massive of atom types
* @param total_types number of different atom types
*
* @return 1 - error in opening file
* @return 2 - error in file format
* @return 3 - memory error
* @return 0 - exit without errors
*/
{
char at_symb[2], tmp_str[256];
int at_ndx, i, j, total_atoms;
FILE *f_inp;
/* at_* temp variables
* total_atoms total atom types
* f_inp input file
*/
f_inp = fopen (input_at, "r");
if (f_inp == NULL)
return 1;
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, "NUMTYPES=%i", num_types);
if (*num_types == 0)
return 2;
else if (*num_types > total_types)
return 3;
total_atoms = 0;
for (i=0; i<*num_types; i++)
{
// read constants
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, "NUMMOL=%i", &num_mol[i]);
if (num_mol[i] == 0)
return 2;
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, "NUMAT=%i", &num_atoms[i]);
if (num_atoms[i] == 0)
return 2;
else if ((total_atoms + num_atoms[i]) > total_types)
return 2;
// read atoms
for (j=0; j<num_atoms[i]; j++)
{
fgets (tmp_str, 256, f_inp);
at_ndx = -1;
sscanf (tmp_str, "%2s=%i", at_symb, &at_ndx);
if (at_ndx == -1)
return 2;
ch_atom_types[2*total_atoms+2*j+0] = at_symb[0];
ch_atom_types[2*total_atoms+2*j+1] = at_symb[1];
atom_types[total_atoms+j] = at_ndx;
}
total_atoms += num_atoms[i];
}
fclose (f_inp);
return 0;
}

354
mathmech/mm/src/coords.c Normal file
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/**
* @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)
/**
* @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_* 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;
/// <pre> reading file </pre>
inp = fopen (filename, "r");
if (inp == NULL)
return 1;
ref_mol = -1;
fscanf (inp, "%i", &atoms);
not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
fgets (file_string, 256, inp);
for (i=0; i<atoms; i++)
{
fgets (file_string, 256, inp);
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:
// mode == 0 (selected atoms)
for (j=0; j<type_inter; j++)
if (cur_at_type == 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];
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;
case 1:
// 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];
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;
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);
/// <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
ref_mol = label_mol[0];
for (i=0; i<3; i++)
ref[i] = coords[3*0+i];
for (i=0; i<*num_atoms; i++)
{
if (label_mol[i] != ref_mol)
{
ref_mol = label_mol[i];
for (j=0; j<3; j++)
ref[j] = not_tr_coords[3*i+j];
}
for (x=0; x<3; x++)
{
if (ref[x] >= 0.0)
// if xyz >= 0.0 A
{
for (j=0; j<3; j++)
if (j == x)
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
else
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
else
// if xyz < 0.0 A
{
for (j=0; j<3; j++)
if (j == x)
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
else
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
}
for (x=0; x<3; x++)
{
for (y=x+1; y<3; y++)
{
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
// if xyz and xyz >= 0.0 A
{
for (j=0; j<3; j++)
if ((j == x) || (j == y))
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
else
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
if ((ref[x] < 0.0) && (ref[y] < 0.0))
// if xyz and xyz < 0.0 A
{
for (j=0; j<3; j++)
if ((j == x) || (j == y))
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
else
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
}
for (y=0; y<3; y++)
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
// if xyz OR xyz >= 0.0
{
for (j=0; j<3; j++)
{
if (j == x)
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
if (j == y)
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
if ((j != x) && (j != y))
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
}
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
}
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
// 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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
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
{
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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
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
{
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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
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
{
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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
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
{
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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
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
{
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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
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
{
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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
// 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];
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
label_mol[tr_num_atoms] = label_mol[i];
type_atoms[tr_num_atoms] = type_atoms[i];
tr_num_atoms++;
}
}
/// <pre> free memory </pre>
free (not_tr_coords);
return 0;
}

51
mathmech/mm/src/envir_search.c Normal file
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/**
* @file
*/
#include <math.h>
/**
* @fn search_envir
*/
int search_envir (const int num_of_mol, const int num_mol, const float *centr_coords,
const double rad, int *needed_mol, int *num_needed_mol)
/**
* @brief function that searchs environment
* @code
* search_envir (number_of_molecule, num_mol, centr_coords, rad, needed_mol,
* &num_needed_mol);
* @endcode
*
* @param num_of_mol number of molecule
* @param num_mol number of molecules
* @param centr_coords massive of centered coordinates
* @param rad radius of environment sphere
* @param needed_mol massive of number of needed molecules
* @param num_needed_mol number of needed molecules
*
* @return 0 - exit without errors
*/
{
float r;
int i;
/* r radius
*/
*num_needed_mol = 0;
for (i=0; i<8*num_mol; i++)
{
r = sqrt (pow ((centr_coords[3*i+0]-centr_coords[3*8*(num_of_mol-1)+0]), 2) +
pow ((centr_coords[3*i+1]-centr_coords[3*8*(num_of_mol-1)+1]), 2) +
pow ((centr_coords[3*i+2]-centr_coords[3*8*(num_of_mol-1)+2]), 2));
if (r < rad)
{
needed_mol[*num_needed_mol] = i;
*num_needed_mol = *num_needed_mol + 1;
}
}
return 0;
}

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mathmech/mm/src/graph.c Normal file
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/**
* @file
*/
#include <math.h>
#include <stdlib.h>
/**
* @fn check_cycle
*/
int check_cycle (const int N, const int *pn)
/**
* @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 = 0;
for (i=1; i<N; i++)
cycle += i*pn[i];
// 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)
/**
* @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
*/
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
n = pow (2, N);
for (i=0; i<n; i++)
{
cur_N = 0;
for (j=0; j<N; j++)
if ( i & (1 << j))
{
vertex[cur_N] = j;
cur_N++;
}
if ((cur_N > 2) && (cur_N <= depth))
{
// copy connectivity matrix
cycle = 1;
for (j=0; j<cur_N; j++)
{
p = 0;
for (k=0; k<cur_N; k++)
p += matrix[vertex[j]*N+vertex[k]];
if (p != 2)
cycle = 0;
}
// analyze subgraph
if (cycle == 1)
n_cycle[cur_N-3]++;
}
}
free (vertex);
return 0;
}
/**
* @fn check_tail
*/
int check_tail (const int *pn)
/**
* @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)
/**
* @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 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
pn = (int *) malloc (N * sizeof (int));
n_cycle = (int *) malloc ((depth - 2) * sizeof (int));
if ((pn == NULL) ||
(n_cycle == NULL))
return 1;
for (i=0; i<N; i++)
pn[i] = 0;
for (i=0; i<N; i++)
{
p = 0;
for (j=0; j<N; j++)
p += matrix[i*N+j];
pn[p]++;
}
iso[0] = check_tail (pn);
iso[1] = check_cycle (N, pn);
for (i=2; i<max_depth; i++)
iso[i] = 0;
if (iso[1] > 0)
{
check_cycle_size (N, matrix, depth, n_cycle);
for (i=0; i<depth-2; i++)
iso[i+2] = n_cycle[i];
}
// free memory
free (n_cycle);
free (pn);
return 0;
}

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mathmech/mm/src/main.c Normal file
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/**
* @file
*/
/**
* @mainpage libmm
* @image latex ./logo.png
*
* @section intro_sec Introduction
*
* <b>About this program</b>:
* <ul>
* <li>Library for mathmech
* </ul>
*
* <b>Developer</b>:
* <ul>
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
*</ul>
* <b>License</b>:
* <ul>
* <li>GPL
* </ul>
*
* @page Install
*
* @section Requirements Requirements
* The application mmlib 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.1.1.1 (2013-09-03)
* <ul>
* <li>optimization
* </ul>
* V.1.1.0 (2013-09-02)
* <ul>
* <li>added help window
* <li>added help docs
* <li>small bug fixes
* </ul>
* V.1.0.3 (2013-08-30)
* <ul>
* <li>bug fixes
* </ul>
* V.1.0.1 (2013-07-27)
* <ul>
* <li>initial release
* </ul>
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <mathmech/atom_types.h>
#include <mathmech/coords.h>
#include <mathmech/envir_search.h>
#include <mathmech/graph.h>
#include <mathmech/messages.h>
#include <mathmech/print_struct.h>
#include <mathmech/print_trj.h>
#include <mathmech/radf.h>
#include <mathmech/radf_proc.h>
#include <mathmech/read_agl.h>
#include <mathmech/read_gmx.h>
#include <mathmech/read_puma.h>
#include <mathmech/select_mol.h>
#include <mathmech/set_center.h>
#include <mathmech/stat_print.h>
#include <mathmech/stat_select.h>
#include <mathmech/stat_sort.h>
#include <mathmech/summary_stat.h>
/**
* @fn main
*/
int main(int argc, char *argv[])
/**
* @return 0 - exit without errors
*/
{
return 0;
}

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/**
* @file
*/
#include <stdio.h>
#include <time.h>
/**
* @fn message
*/
int message (const int log, const int mode, const char *text, FILE *output)
/**
* @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 1 - unknown mode
* @return 0 - exit without errors
*/
{
char out[4096];
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,
aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode);
fputs (time_str, output);
}
switch (mode)
{
case 0:
sprintf (out, "Start program: '%s'\n", text);
break;
case 1:
sprintf (out, "Checking errors\n");
break;
case 2:
sprintf (out, "Errors are not detected\n");
break;
case 3:
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);
break;
case 6:
sprintf (out, "Processing\n");
break;
case 7:
sprintf (out, "Open file: '%s'\n", text);
break;
case 8:
sprintf (out, "%s", text);
break;
case 9:
sprintf (out, "%6cSize of variables was changed successfully\n", ' ');
break;
case 10:
sprintf (out, "%6cConnectivity matrix was created successfully\n", ' ');
break;
case 11:
sprintf (out, "%6cConnectivity matrix was processed successfully\n", ' ');
break;
case 12:
sprintf (out, "%6cResult was printed to file '%s' successfully\n", ' ', text);
break;
case 13:
sprintf (out, "End of processing\n");
break;
case 14:
sprintf (out, "Print result to file '%s'\n", text);
break;
case 15:
sprintf (out, "Free memory\n");
break;
case 16:
sprintf (out, "Exiting without errors\n");
break;
case 17:
sprintf (out, "Something wrong!\nSee '%s -h' for more details\n", text);
break;
case 18:
sprintf (out, "File '%s' not found\nError\n", text);
break;
case 19:
sprintf (out, "Memory error\n");
break;
case 20:
sprintf (out, "%6cCenter of molecules was set successfully\n", ' ');
break;
case 21:
sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
break;
case 22:
sprintf (out, "%6cRADF was appended successfully\n", ' ');
break;
default:
return 1;
break;
}
fputs (out, output);
return 0;
}

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/**
* @file
*/
#include <stdio.h>
/**
* @fn print_structure
*/
int print_structure (const char *output, const int num_needed_mol, const int *needed_mol,
const int num_atoms, const int *label_mol, const char *ch_type_atoms,
const float *coords)
/**
* @brief function that prints structure to pdb file
* @code
* print_structure (output, num_needed_mol, needed_mol, num_atoms, label_mol,
* char_type_atoms, coords);
* @endcode
*
* @param output output file name
* @param num_needed_mol number of needed molecules
* @param needed_mol massive of number of needed molecules
* @param num_atoms number of atoms
* @param label_mol massive of numbers of molecule for atoms
* @param ch_type_atoms massive of char atom types
* @param coords massive of coordinates
*
* @return 0 - exit without errors
*/
{
int cur_atom, cur_atom_num, cur_mol, i, j;
FILE *f_out;
/* cur_atom current atom
* cur_atom_num true atom number
* cur_mol current molecule
* f_out output file
*/
cur_atom = 1;
f_out = fopen (output, "w");
for (i=0; i<num_needed_mol; i++)
for (j=0; j<8*num_atoms; j++)
{
if (j < num_atoms)
{
cur_mol = 0;
cur_atom_num = j;
}
else
{
cur_mol = ((j - num_atoms) % 7) + 1;
cur_atom_num = (j - num_atoms) / 7;
}
if (needed_mol[i] == (8*label_mol[j]+cur_mol))
{
fprintf(f_out, "ATOM %5i %c%c MOL %4i %8.3f%8.3f%8.3f\n", cur_atom,
ch_type_atoms[2*cur_atom_num+0], ch_type_atoms[2*cur_atom_num+1],
i+1, coords[3*j+0], coords[3*j+1], coords[3*j+2]);
cur_atom++;
}
}
fclose (f_out);
return 0;
}

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/**
* @file
*/
#include <stdio.h>
/**
* @fn printing_trj
*/
int printing_trj (const char *filename, const int atoms, const int num_types, const int *num_mol,
const int *num_atoms, const char *ch_atom_types, const int *atom_types,
const float *coords)
/**
* @brief function that prints trajectory snapshots
* @code
* printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types,
* atom_types, coords);
* @endcode
*
* @param filename output file name
* @param atoms number of atoms in system
* @param num_types number of molecule types
* @param num_mol massive of number of molecule of selected type
* @param num_atoms massive of number of atoms of selected molecule
* @param ch_atom_types massive of char atom types
* @param atom_types massive of atom types
* @param coords massive of coordinates
*
* @return 0 - exit without errors
*/
{
int cur_mol, cur_type[2], i, j, k, l;
FILE *f_out;
/* cur_mol number of current molecule
* cur_type number of current atom type
* f_out output file
*/
cur_mol = 1;
f_out = fopen (filename, "w");
fprintf (f_out, " %6i\n", atoms);
i = 0;
while (i < atoms)
{
cur_type[0] = 0;
for (j=0; j<num_types; j++)
{
for (k=0; k<num_mol[j]; k++)
{
cur_type[1] = cur_type[0];
for (l=0; l<num_atoms[j]; l++)
{
fprintf (f_out, "%5i %c%c %12.6f%12.6f%12.6f %2i %4i\n", i+1,
ch_atom_types[2*cur_type[1]+0], ch_atom_types[2*cur_type[1]+1], coords[3*i+0],
coords[3*i+1], coords[3*i+2], atom_types[cur_type[1]], cur_mol);
cur_type[1]++;
i++;
}
cur_mol++;
}
cur_type[0] += num_atoms[j];
}
}
fclose (f_out);
return 0;
}

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/**
* @file
*/
#include <math.h>
// pi
#if !defined __USE_BSD && !defined __USE_XOPEN
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif /* __USE_BSD && __USE_XOPEN */
#endif /* M_PI */
/**
* @fn search_rdf
*/
int search_rdf (const int num_atoms, const int *type_atoms, const int *label_mol,
const float *coords, const double r_min, const double r_max,
const double r_step, int *radf)
/**
* @brief function that searchs molecule for rdf massive
* @code
* search_rdf (num_atoms, type_atoms, label_mol, coords, r_min, r_max, r_step, radf);
* @endcode
*
* @param num_atoms number of atoms
* @param type_atoms massive of atom types
* @param label_mol massive of numbers of molecule for atoms
* @param coords massive of coordinates
* @param r_min minimal radius
* @param r_max maximal radius
* @param r_step radius step
* @param radf not normed RDF
*
* @return 0 - exit without errors
*/
{
float r;
int i, j, k;
/* r radius
*/
for (i=0; i<num_atoms; i++)
for (j=0; j<8*num_atoms; j++)
if (((type_atoms[i] == 0) && (type_atoms[j] == 1)) ||
((type_atoms[i] == 1) && (type_atoms[j] == 0)))
{
r = sqrt (pow ((coords[3*i+0] - coords[3*j+0]), 2) +
pow ((coords[3*i+1] - coords[3*j+1]), 2) +
pow ((coords[3*i+2] - coords[3*j+2]), 2));
if ((r >= r_min) && (r <= r_max))
{
k = (r - r_min) / r_step;
radf[k]++;
}
}
return 0;
}
/**
* @fn search_rdf_centr
*/
int search_rdf_centr (const int num_atoms, const int *type_atoms, const int *label_mol,
const float *coords, const double r_min, const double r_max,
const double r_step, int *radf)
/**
* @brief function that searchs molecule for rdf massive by centered coordinates
* @code
* search_rdf_centr (num_atoms, type_atoms, label_mol, coords, r_min, r_max, r_step,
* radf);
* @endcode
*
* @param num_atoms number of atoms
* @param type_atoms massive of atom types
* @param label_mol massive of numbers of molecule for atoms
* @param coords massive of coordinates
* @param r_min minimal radius
* @param r_max maximal radius
* @param r_step radius step
* @param radf not normed RDF
*
* @return 0 - exit without errors
* @return 1 - error in set center (missing atoms)
*/
{
float r, cur_coords[2][3];
int coef, cur_at, i, j, k, l;
/* cur_coords centered coordinates
* r radius
* coef ==1 if j<num_atoms, ==7 if j>=num_atoms
* cur_at number of founded atoms
*/
for (i=0; i<num_atoms; i++)
if ((type_atoms[i] == 0) || (type_atoms[i] == 3))
for (j=0; j<8*num_atoms; j++)
if (((type_atoms[i] == 0) && (type_atoms[j] == 3)) ||
((type_atoms[i] == 3) && (type_atoms[j] == 0)))
{
// set center for i-molecule
for (l=0; l<3; l++)
cur_coords[0][l] = coords[3*i+l];
cur_at = 1;
for (k=1; k<6; k++)
if (label_mol[i+k] == label_mol[i])
if ((type_atoms[i+k] == type_atoms[i] + 1) ||
(type_atoms[i+k] == type_atoms[i] + 2))
{
cur_at++;
for (l=0; l<3; l++)
cur_coords[0][l] += coords[3*(i+k)+l];
}
if (cur_at == 3)
for (l=0; l<3; l++)
cur_coords[0][l] = cur_coords[0][l] / cur_at;
else
return 1;
// set center for j-molecule
for (l=0; l<3; l++)
cur_coords[1][l] = coords[3*j+l];
cur_at = 1;
if (j < num_atoms)
coef = 1;
else
coef = 7;
for (k=1; k<6; k++)
if (label_mol[j+coef*k] == label_mol[j])
if ((type_atoms[j+coef*k] == type_atoms[j] + 1) ||
(type_atoms[j+coef*k] == type_atoms[j] + 2))
{
cur_at++;
for (l=0; l<3; l++)
cur_coords[1][l] += coords[3*(j+coef*k)+l];
}
if (cur_at == 3)
for (l=0; l<3; l++)
cur_coords[1][l] = cur_coords[1][l] / cur_at;
else
return 1;
r = sqrt (pow ((cur_coords[0][0] - cur_coords[1][0]), 2) +
pow ((cur_coords[0][1] - cur_coords[1][1]), 2) +
pow ((cur_coords[0][2] - cur_coords[1][2]), 2));
if ((r >= r_min) && (r <= r_max))
{
k = (r - r_min) / r_step;
radf[k]++;
}
}
return 0;
}
/**
* @fn search_radf
*/
int search_radf (const int num_atoms, const int *type_atoms, const int *label_mol,
const float *coords, const double r_min, const double r_max,
const double r_step, const double ang_min, const double ang_max,
const double ang_step, int *radf)
/**
* @brief function that searchs molecule for radf massive
* @code
* search_radf (num_atoms, type_atoms, label_mol, coords, r_min, r_max, r_step,
* ang_min, ang_max, ang_step, radf);
* @endcode
*
* @param num_atoms number of atoms
* @param type_atoms massive of atom types
* @param label_mol massive of numbers of molecule for atoms
* @param coords massive of coordinates
* @param r_min minimal radius
* @param r_max maximal radius
* @param r_step radius step
* @param ang_min minimal angle
* @param ang_max maximal angle
* @param ang_step anlge step
* @param radf not normed RADF
*
* @return 0 - exit without errors
* @return 1 - error in set center (missing atoms)
*/
{
float ang, cos_ang, cur_coords[2][3], normal[2][3], r;
int coef, cur_at, i, j, k, l, n, n_max, plane_index[6];
/* ang angle
* cur_coords centered coordinates
* normal normal to planes
* r radius
* coef ==1 if j<num_atoms, ==7 if j>=num_atoms
* cur_at number of founded atoms
* n_max range of angles
* plane_index atoms forming plane
*/
for (i=0; i<num_atoms; i++)
if ((type_atoms[i] == 0) || (type_atoms[i] == 3))
for (j=0; j<8*num_atoms; j++)
if (((type_atoms[i] == 0) && (type_atoms[j] == 3)) ||
((type_atoms[i] == 3) && (type_atoms[j] == 0)))
{
// set center for i-molecule
plane_index[type_atoms[i]] = i;
for (l=0; l<3; l++)
cur_coords[0][l] = coords[3*i+l];
cur_at = 1;
for (k=1; k<6; k++)
if (label_mol[i+k] == label_mol[i])
if ((type_atoms[i+k] == type_atoms[i] + 1) ||
(type_atoms[i+k] == type_atoms[i] + 2))
{
cur_at++;
plane_index[type_atoms[i+k]] = i + k;
for (l=0; l<3; l++)
cur_coords[0][l] += coords[3*(i+k)+l];
}
if (cur_at == 3)
for (l=0; l<3; l++)
cur_coords[0][l] = cur_coords[0][l] / cur_at;
else
return 1;
// set center for j-molecule
plane_index[type_atoms[j]] = j;
for (l=0; l<3; l++)
cur_coords[1][l] = coords[3*j+l];
cur_at = 1;
if (j < num_atoms)
coef = 1;
else
coef = 7;
for (k=1; k<6; k++)
if (label_mol[j+coef*k] == label_mol[j])
if ((type_atoms[j+coef*k] == type_atoms[j] + 1) ||
(type_atoms[j+coef*k] == type_atoms[j] + 2))
{
cur_at++;
plane_index[type_atoms[j+coef*k]] = j + coef * k;
for (l=0; l<3; l++)
cur_coords[1][l] += coords[3*(j+coef*k)+l];
}
if (cur_at == 3)
for (l=0; l<3; l++)
cur_coords[1][l] = cur_coords[1][l] / cur_at;
else
return 1;
r = sqrt (pow ((cur_coords[0][0] - cur_coords[1][0]), 2) +
pow ((cur_coords[0][1] - cur_coords[1][1]), 2) +
pow ((cur_coords[0][2] - cur_coords[1][2]), 2));
// define planes
normal[0][0] = (coords[3*plane_index[1]+1] - coords[3*plane_index[0]+1]) *
(coords[3*plane_index[2]+2] - coords[3*plane_index[0]+2]) -
(coords[3*plane_index[1]+2] - coords[3*plane_index[0]+2]) *
(coords[3*plane_index[2]+1] - coords[3*plane_index[0]+1]);
normal[0][1] = (coords[3*plane_index[1]+2] - coords[3*plane_index[0]+2]) *
(coords[3*plane_index[2]+0] - coords[3*plane_index[0]+0]) -
(coords[3*plane_index[1]+0] - coords[3*plane_index[0]+0]) *
(coords[3*plane_index[2]+2] - coords[3*plane_index[0]+2]);
normal[0][2] = (coords[3*plane_index[1]+0] - coords[3*plane_index[0]+0]) *
(coords[3*plane_index[2]+1] - coords[3*plane_index[0]+1]) -
(coords[3*plane_index[1]+1] - coords[3*plane_index[0]+1]) *
(coords[3*plane_index[2]+0] - coords[3*plane_index[0]+0]);
normal[1][0] = (coords[3*plane_index[4]+1] - coords[3*plane_index[3]+1]) *
(coords[3*plane_index[5]+2] - coords[3*plane_index[3]+2]) -
(coords[3*plane_index[4]+2] - coords[3*plane_index[3]+2]) *
(coords[3*plane_index[5]+1] - coords[3*plane_index[3]+1]);
normal[1][1] = (coords[3*plane_index[4]+2] - coords[3*plane_index[3]+2]) *
(coords[3*plane_index[5]+0] - coords[3*plane_index[3]+0]) -
(coords[3*plane_index[4]+0] - coords[3*plane_index[3]+0]) *
(coords[3*plane_index[5]+2] - coords[3*plane_index[3]+2]);
normal[1][2] = (coords[3*plane_index[4]+0] - coords[3*plane_index[3]+0]) *
(coords[3*plane_index[5]+1] - coords[3*plane_index[3]+1]) -
(coords[3*plane_index[4]+1] - coords[3*plane_index[3]+1]) *
(coords[3*plane_index[5]+0] - coords[3*plane_index[3]+0]);
cos_ang = (normal[0][0] * normal[1][0] + normal[0][1] * normal[1][1] + normal[0][2] * normal[1][2]) /
(sqrt (pow ((normal[0][0]), 2) + pow ((normal[0][1]), 2) + pow ((normal[0][2]), 2)) *
sqrt (pow ((normal[1][0]), 2) + pow ((normal[1][1]), 2) + pow ((normal[1][2]), 2)));
ang = 180 / M_PI * acos (cos_ang);
if (ang > 90)
ang = 180 - ang;
n_max = (ang_max - ang_min) / ang_step;
if ((r >= r_min) && (r <= r_max))
if ((ang >= ang_min) && (ang <= ang_max))
{
k = (r - r_min) / r_step;
n = (ang - ang_min) / ang_step;
radf[n_max*k+n]++;
}
}
return 0;
}

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/**
* @file
*/
#include <math.h>
#include <stdio.h>
// pi
#if !defined __USE_BSD && !defined __USE_XOPEN
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif /* __USE_BSD && __USE_XOPEN */
#endif /* M_PI */
/**
* @fn print_result
*/
int print_result (const char *output, const int matrix, const int mode,
const int step, const int num_atoms, const double r_min,
const double r_max, const double r_step, const double ang_min,
const double ang_max, const double ang_step, const float *cell,
const int *radf)
/**
* @brief function that print result to output file
* @code
* print_result (output, matrix, mode, step, num_atoms, r_min, r_max, r_step, ang_min,
* ang_max, ang_step, cell, radf);
* @endcode
*
* @param output output file name
* @param matrix status of matrix-mode
* @param mode 1 - if RDF, 2 - if RDF for center mass, 3 - if RADF
* @param step $(to - from + 1)
* @param num_atoms number of atoms
* @param r_min minimal radius
* @param r_max maximal radius
* @param r_step radius step
* @param ang_min minimal angle
* @param ang_max maximal angle
* @param ang_step angle step
* @param cell cell size
* @param radf not normed RADF
*
* @return 0 - exit without errors
*/
{
float ang, dv, norm, r, ro;
int i, j, k, n;
FILE *f_out;
/* ang angle
* dv volume
* norm normed RDF
* r radius
* ro density
* f_out output file
*/
f_out = fopen (output, "a");
fprintf (f_out, "SUMMARY STATISTIC\n");
switch (mode)
{
case 0:
if (matrix == 0)
fprintf (f_out, "| r | dV | RDF | RDFnorm |\n------------------------------------------\n");
k = (r_max - r_min) / r_step;
for (i=0; i<k; i++)
{
r = r_min + (0.5 + i) * r_step;
dv = 4 * M_PI * pow (r, 2) * r_step;
ro = num_atoms / (2 * cell[0] * cell[1] * cell[2]);
norm = radf[i] / (dv * ro * num_atoms * step);
if (matrix == 0)
fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
else
fprintf (f_out, " %9.4f %9.6f\n", r, norm);
}
fprintf (f_out, "------------------------------------------\n");
break;
case 1:
if (matrix == 0)
fprintf (f_out, "| r | dV | RDF | RDFnorm |\n------------------------------------------\n");
k = (r_max - r_min) / r_step;
for (i=0; i<k; i++)
{
r = r_min + (0.5 + i) * r_step;
dv = 4 * M_PI * pow (r, 2) * r_step;
ro = num_atoms / (3 * 2 * cell[0] * cell[1] * cell[2]);
norm = radf[i] / (dv * ro * num_atoms / 3 * step);
if (matrix == 0)
fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
else
fprintf (f_out, " %9.4f %9.6f\n", r, norm);
}
fprintf (f_out, "------------------------------------------\n");
break;
case 2:
if (matrix == 0)
fprintf (f_out, "| r | ang | dV | RDF | RDFnorm |\n----------------------------------------------------\n");
k = (r_max - r_min) / r_step;
n = (ang_max - ang_min) / ang_step;
if (matrix == 1)
{
fprintf (f_out, " r\\ang ");
for (j=0; j<n; j++)
fprintf (f_out, " %9.2f", ang_min+(0.5+j)*ang_step);
fprintf (f_out, "\n");
}
for (i=0; i<k; i++)
{
if (matrix == 1)
fprintf (f_out, " %9.4f", r);
for (j=0; j<n; j++)
{
r = r_min + (0.5 + i) * r_step;
ang = ang_min + (0.5 + j) * ang_step;
dv = 4 * M_PI * pow (r, 2) * sin (M_PI * ang / 180) * r_step * (M_PI * ang_step / 180);
ro = num_atoms / (3 * 2 * cell[0] * cell[1] * cell[2]);
norm = radf[n*i+j] / (dv * ro * num_atoms / 3 * step);
if (matrix == 0)
fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[n*i+j] / 2, norm);
else
fprintf (f_out, " %9.6f", norm);
}
if (matrix == 1)
fprintf (f_out, "\n");
}
fprintf (f_out, "----------------------------------------------------\n");
break;
}
fclose (f_out);
return 0;
}

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/**
* @file
*/
/* Library for reading agglomerate from statgen-file
*
* Usage:
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol)
*/
#include <stdio.h>
/**
* @fn reading_agl
*/
int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol)
/**
* @brief function that reads agglomerate from statgen-formated file
* @code
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol);
* @endcode
*
* @param aglinp agglomerate file name
* @param num_needed_mol number of needed molecules
* @param agl_class agglomerate class
* @param needed_mol massive of numbed of needed molecules
*
* @return 0 - exit without errors
*/
{
char connect[256], tmp_str[256];
int i;
FILE *f_agl;
/* connect - connectivity matrix for molecule
* f_agl - agglomerate file
*/
f_agl = fopen (aglinp, "r");
fgets (tmp_str, 256, f_agl);
sscanf (tmp_str, "AGL=%i=%s", num_needed_mol, agl_class);
for (i=0; i<*num_needed_mol; i++)
{
fgets (tmp_str, 256, f_agl);
sscanf (tmp_str, "%i=%s", &needed_mol[i], connect);
}
fclose (f_agl);
return 0;
}

154
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/**
* @file
*/
#include <math.h>
#include <stdio.h>
#include <mathmech/print_trj.h>
/**
* @fn translate_coords
*/
int translate_coords (const float coords, const float cell, float *trans)
/**
* @brief funtion that translates coordinate
* @code
* translate_coords (coords[3*i+j], cell[j], trans);
* @endcode
*
* @param coords coordinate
* @param cell cell size
* @param trans massive of translated coordinates
*
* @return 0 - exit without errors
*/
{
trans[0] = coords;
trans[1] = coords - cell;
trans[2] = coords + cell;
return 0;
}
/**
* @fn rw_gmx
*/
int rw_gmx (const char *input, const int step, const char *output, const int num_types,
const int *num_mol, const int *num_atoms, const char *ch_atom_types,
const int *atom_types, float *coords)
/**
* @brief function that read GROMACS trajectory file and write to output
* @code
* rw_gmx (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
* atom_types, coords);
* @endcode
*
* @param input input file name
* @param step number of trajectory steps
* @param output mask of output files
* @param num_types number of molecule types
* @param num_mol massive of number of molecule of selected type
* @param num_atoms massive of number of atoms of selected molecule
* @param ch_atom_types massive of char atom types
* @param atom_types massive of atom types
* @param coords massive of coordinates
*
* @return 1 - file does not exist
* @return 0 - exit without errors
*/
{
char filename[256], tmp_str[256];
float cell[3], trans[3], r_min;
int atoms, i, j, k, l, m, n;
FILE *f_inp;
/* filename output file name
* cell cell size
* trans translated coordinates
* r_min minimal radius
* atom number of atoms
* f_inp input file
*/
f_inp = fopen (input, "r");
if (f_inp == NULL)
return 1;
for (i=0; i<step; i++)
{
// initial variables
sprintf (filename, "%s.%03i", output, i+1);
fgets (tmp_str, 256, f_inp);
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, " natoms=%i%s", &atoms, tmp_str);
fgets (tmp_str, 256, f_inp);
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, " box[ 0]={%f%s", &cell[0], tmp_str);
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, " box[ 1]={%f,%f%s", &cell[1], &cell[1], tmp_str);
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, " box[ 2]={%f,%f,%f%s", &cell[2], &cell[2], &cell[2], tmp_str);
fgets (tmp_str, 256, f_inp);
for (j=0; j<3; j++)
cell[j] = 10 * cell[j];
// coordinates
for (j=0; j<atoms; j++)
{
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, " x[%i]={%f,%f,%f%s", &k, &coords[3*j+0], &coords[3*j+1],
&coords[3*j+2], tmp_str);
for (k=0; k<3; k++)
coords[3*j+k] = 10 * coords[3*j+k];
}
// velocities
fgets (tmp_str, 256, f_inp);
for (j=0; j<atoms; j++)
fgets (tmp_str, 256, f_inp);
// processing coordinates
j = 0;
while (j < atoms)
for (k=0; k<num_types; k++)
for (l=0; l<num_mol[k]; l++)
{
for (m=1; m<num_atoms[k]; m++)
for (n=0; n<3; n++)
{
r_min = fabs (coords[3*(j+m)+n] - coords[3*j+n]);
translate_coords (coords[3*(j+m)+n], cell[n], trans);
if (fabs (trans[1] - coords[3*j+n]) < r_min)
coords[3*(j+m)+n] = trans[1];
if (fabs (trans[2] - coords[3*j+n]) < r_min)
coords[3*(j+m)+n] = trans[2];
}
j += num_atoms[k];
}
j = 0;
while (j < atoms)
for (k=0; k<num_types; k++)
for (l=0; l<num_mol[k]; l++)
{
for (m=0; m<3; m++)
{
while (coords[3*j+m] > cell[m]/2)
for (n=j; n<j+num_atoms[k]; n++)
coords[3*n+m] -= cell[m];
while (coords[3*j+m] < -cell[m]/2)
for (n=j; n<j+num_atoms[k]; n++)
coords[3*n+m] += cell[m];
}
j += num_atoms[k];
}
// write to output
printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types,
atom_types, coords);
}
fclose (f_inp);
return 0;
}

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/**
* @file
*/
#include <stdio.h>
#include <mathmech/print_trj.h>
/**
* @fn rw_puma
*/
int rw_puma (const char *input, const int step, const char *output, const int num_types,
const int *num_mol, const int *num_atoms, const char *ch_atom_types,
const int *atom_types, float *coords)
/**
* @brief function that read PUMA trajectory file and write to output
* @code
* rw_puma (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
* atom_types, coords);
* @endcode
*
* @param input input file name
* @param step number of trajectory steps
* @param output mask of output files
* @param num_types number of molecule types
* @param num_mol massive of number of molecule of selected type
* @param num_atoms massive of number of atoms of selected molecule
* @param ch_atom_types massive of char atom types
* @param atom_types massive of atom types
* @param coords massive of coordinates
*
* @return 1 - file does not exist
* @return 0 - exit without errors
*/
{
char filename[256], tmp_str[256];
float cell[3];
int atoms, i, j, k, l, m, n;
FILE *f_inp;
/* filename output file name
* cell cell size
* atom number of atoms
* f_inp input file
*/
f_inp = fopen (input, "r");
if (f_inp == NULL)
return 1;
for (i=0; i<step; i++)
{
// initial variables
sprintf (filename, "%s.%03i", output, i+1);
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, "%s%s%i%s", tmp_str, tmp_str, &atoms, tmp_str);
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, "%f%f%f", &cell[0], &cell[1], &cell[2]);
// coordinates
for (j=0; j<atoms; j++)
{
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, "%f%f%f", &coords[3*j+0], &coords[3*j+1], &coords[3*j+2]);
}
fgets (tmp_str, 256, f_inp);
// processing coordinates
j = 0;
while (j < atoms)
for (k=0; k<num_types; k++)
for (l=0; l<num_mol[k]; l++)
{
for (m=0; m<3; m++)
{
while (coords[3*j+m] > cell[m]/2)
for (n=j; n<j+num_atoms[k]; n++)
coords[3*n+m] -= cell[m];
while (coords[3*j+m] < -cell[m]/2)
for (n=j; n<j+num_atoms[k]; n++)
coords[3*n+m] += cell[m];
}
j += num_atoms[k];
}
// write to output
printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types,
atom_types, coords);
}
fclose (f_inp);
return 0;
}

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/**
* @file
*/
#include <math.h>
/**
* @fn select_molecule
*/
int select_molecule (const float *centr_coords, const int num_needed_mol, int *needed_mol)
/**
* @brief function that selects molecules from array of translated molecules
* @code
* select_molecule (centr_coords, num_needed_mol, needed_mol);
* @endcode
*
* @param centr_coords massive of centered coordinates
* @param num_needed_mol number of needed molecules
* @param needed_mol massive of number of needed molecules
*
* @return 0 - exit without errors
*/
{
float r, ref[3], rmin;
int i, j, jmin;
/* r radius
* ref coordinated of center mass
* rmin minimal radius
* jmin index of the nearest molecule
*/
// set first molecule
needed_mol[0] = 0;
for (i=0; i<3; i++)
ref[i] = centr_coords[3*8*0+0+i];
// work block
for (i=1; i<num_needed_mol; i++)
{
rmin = sqrt (pow ((centr_coords[3*8*i+0+0] - ref[0]), 2) + \
pow ((centr_coords[3*8*i+0+1] - ref[1]), 2) + \
pow ((centr_coords[3*8*i+0+2] - ref[2]), 2));
jmin = 0;
for (j=1; j<8; j++)
{
r = sqrt (pow ((centr_coords[3*8*i+j+0] - ref[0]), 2) + \
pow ((centr_coords[3*8*i+j+1] - ref[1]), 2) + \
pow ((centr_coords[3*8*i+j+2] - ref[2]), 2));
if (r < rmin)
{
rmin = r;
jmin = j;
}
}
// add molecule
needed_mol[i] = 8 * i + jmin;
// update ref
for (j=0; j<3; j++)
{
ref[j] += centr_coords[3*8*i+jmin+j];
ref[j] = ref[j] / 2;
}
}
return 0;
}

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/**
* @file
*/
/**
* @fn set_center
*/
int set_center (const int num_atoms, const int num_mol, const int *label_mol,
const float *coords, float *centr_coords)
/**
* @brief function that searchs center mass of molecules
* @code
* set_center (num_of_atoms, num_of_molecules, label_molecules, coords, centr_coords);
* @endcode
*
* @param num_atoms number of atoms
* @param num_mol number of molecules
* @param label_mol massive of numbers of molecule for atoms
* @param coords massive of coordinates
* @param centr_coords massive of centered coordinates
*
* @return 0 - exit without errors
*/
{
int at_in_mol, cur_mol, i, j, k;
/* at_int_mol number of atoms in molecule
* cur_mol current molecule
*/
for (i=0; i<8*num_mol; i++)
for (j=0; j<3; j++)
centr_coords[i*3+j] = 0.0;
for (i=0; i<8*num_atoms; i++)
{
if (i < num_atoms)
cur_mol = 0;
else
cur_mol = ((i - num_atoms) % 7) + 1;
for (j=0; j<3; j++)
centr_coords[3*(8*label_mol[i]+cur_mol)+j] += coords[3*i+j];
}
at_in_mol = 0;
cur_mol = 0;
for (i=0; i<num_atoms; i++)
if (cur_mol != label_mol[i])
{
for (j=0; j<8; j++)
for (k=0; k<3; k++)
centr_coords[3*(8*cur_mol+j)+k] = centr_coords[3*(8*cur_mol+j)+k] / at_in_mol;
at_in_mol = 0;
cur_mol = label_mol[i];
}
else
at_in_mol++;
return 0;
}

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/**
* @file
*/
#include <stdio.h>
#include <stdlib.h>
#include <mathmech/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)
/**
* @brief function that prints agglomerates to output file
* @code
* printing_agl (input_file, output_file, number_of_molecules, true_label_molecules,
* num_of_molecules_in_agglomerates, agglomerates, statistic, max_depth,
* type_of_agglomerate);
* @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 agglomerates
* @param agl massive of agglomerates
* @param stat massive of statistic
* @param max_depth maximum depth for check cycles in graph analyze
* @param type_agl massive of number of agglomerate 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
*/
/// <b>Work blocks</b>
iso = (int *) malloc (max_depth * sizeof (int));
if (iso == NULL)
return 1;
f_out = fopen (output, "a");
/// <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");
/// <pre> print body </pre>
for (i=0; i<num_mol; i++)
if (num_mol_agl[i] > 0)
{
/// <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) ||
(label_matrix == NULL))
return 1;
for (j=0; j<num_mol_agl[i]; j++)
for (k=0; k<num_mol_agl[i]; k++)
matrix[num_mol_agl[i]*j+k] = 0;
for (j=0; j<num_mol_agl[i]; j++)
label_matrix[agl[num_mol*i+j]] = j;
for (j=0; j<num_mol_agl[i]; j++)
for (k=j+1; k<num_mol_agl[i]; k++)
if (connect[num_mol*agl[num_mol*i+j]+agl[num_mol*i+k]] == 1)
{
matrix[label_matrix[agl[num_mol*i+j]]*num_mol_agl[i]+label_matrix[agl[num_mol*i+k]]] = 1;
matrix[label_matrix[agl[num_mol*i+k]]*num_mol_agl[i]+label_matrix[agl[num_mol*i+j]]] = 1;
}
/// <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;
// print class of agglomerate
fprintf (f_out, "AGL=%i=", num_mol_agl[i]);
for (j=0; j<max_depth; j++)
{
// number of tails
if (j == 0)
if ((iso[j] == 0) || ((iso[j] <= 2) && (iso[j] == 0)))
// not branched
type_agl[2]++;
// branched
else
type_agl[3]++;
// number of cycles
else if (j == 1)
if (iso[j] > 0)
// cycle
type_agl[1]++;
else
// linear
type_agl[0]++;
else if (j > 1)
// number of n_cycles
type_agl[j+2] += iso[j];
fprintf (f_out, "%i.", iso[j]);
}
fprintf (f_out, "\n");
for (j=0; j<num_mol_agl[i]; j++)
{
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");
}
/// <pre> free memory </pre>
free (matrix);
free (label_matrix);
}
fprintf (f_out, "---------------------------------------------------\n");
fclose (f_out);
/// <pre> free memory </pre>
free (iso);
return 0;
}

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/**
* @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)
/**
* @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
*/
/// <b>Work blocks</b>
label_inter = (int ***) malloc (num_mol * sizeof (int **));
for (i=0; i<num_mol; i++)
{
label_inter[i] = (int **) malloc (num_mol * sizeof (int *));
for (j=0; j<num_mol; j++)
{
label_inter[i][j] = (int *) malloc (16 * sizeof (int));
for (k=0; k<16; k++)
label_inter[i][j][k] = 0;
}
}
if (label_inter == NULL)
return 1;
/// <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 (label_mol[i] != label_mol[j])
{
r = sqrt (pow ((coords[3*i+0]-coords[3*j+0]), 2) +
pow ((coords[3*i+1]-coords[3*j+1]), 2) +
pow ((coords[3*i+2]-coords[3*j+2]), 2));
for (k=0; k<num_of_inter; k++)
if (crit[16*k+4*type_atoms[i]+type_atoms[j]] != 0.0)
if (r < crit[16*k+4*type_atoms[i]+type_atoms[j]])
{
label_inter[label_mol[i]][label_mol[j]][4*type_atoms[i]+type_atoms[j]] = 1;
label_inter[label_mol[i]][label_mol[j]][4*type_atoms[j]+type_atoms[i]] = 1;
label_inter[label_mol[j]][label_mol[i]][4*type_atoms[i]+type_atoms[j]] = 1;
label_inter[label_mol[j]][label_mol[i]][4*type_atoms[j]+type_atoms[i]] = 1;
}
}
for (i=0; i<num_mol; i++)
for (j=0; j<num_mol; j++)
connect[i*num_mol+j] = 0;
/// <pre> processing of initial connectivity matrix </pre>
for (k=0; k<num_of_inter; k++)
{
// determination of the number of interactions
num_inter = 0;
for (l=0; l<16; l++)
if (crit[16*k+l] != 0.0)
num_inter++;
for (i=0; i<num_mol; i++)
for (j=i+1; j<num_mol; j++)
{
cur_num_inter = 0;
for (l=0; l<16; l++)
cur_num_inter += label_inter[i][j][l];
if (cur_num_inter == num_inter)
{
connect[i*num_mol+j] = 1;
connect[j*num_mol+i] = 1;
}
}
}
/// <pre> free memory</pre>
for (i=0; i<num_mol; i++)
{
for (j=0; j<num_mol; j++)
free (label_inter[i][j]);
free (label_inter[i]);
}
free (label_inter);
return 0;
}

100
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/**
* @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)
/**
* @brief function that processes connectivity matrix
* @code
* proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_agglomerates,
* agglomerates, 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 agglomerates
* @param agl massive of agglomerates
* @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
*/
/// <b>Work blocks</b>
// definition and zeroing
bin = (int *) malloc (num_mol * sizeof (int));
if (bin == NULL)
return 1;
for (i=0; i<num_mol; i++)
{
bin[i] = 1;
stat[i] = 0;
num_mol_agl[i] = 0;
for (j=0; j<num_mol; j++)
agl[num_mol*i+j] = 0;
}
/// <pre> select non-bonded molecules </pre>
for (i=0; i<num_mol; i++)
{
p = 0;
for (j=0; j<num_mol; j++)
p += connect[i*num_mol+j];
if (p == 0)
{
bin[i] = 0;
stat[0]++;
stat_all[0]++;
}
}
/// <pre> unwraping of connectivity matrix </pre>
p = 0;
for (i=0; i<num_mol; i++)
if (bin[i] == 1)
{
agl[num_mol*p+num_mol_agl[p]] = i;
num_mol_agl[p]++;
bin[i] = 0;
for (j=0; j<num_mol_agl[p]; j++)
for (k=0; k<num_mol; k++)
if ((connect[agl[num_mol*p+j]*num_mol+k] == 1) && (bin[k] == 1))
{
agl[num_mol*p+num_mol_agl[p]] = k;
num_mol_agl[p]++;
bin[k] = 0;
}
p++;
}
/// <pre> filling statistic array </pre>
i = 0;
while (num_mol_agl[i] > 0)
{
stat[num_mol_agl[i]-1]++;
stat_all[num_mol_agl[i]-1]++;
i++;
}
/// <pre> free memory </pre>
free (bin);
return 0;
}

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/**
* @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)
/**
* @brief function that prints summary statistic
* @code
* summary_statistic (filename, number_of_step, number_of_molecules, max_depth,
* type_of_agglomerate, 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 agglomerate 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 agglomerates
* p probability of agglomerates
* pn weight probability of agglomerates
* f_out output file
*/
index = 0;
for (i=0; i<num_mol; i++)
if (stat_all[i] != 0)
index = i;
// 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
x = stat_all[i];
y = step;
conc = x / y;
// calculating probabilityes
x = (i + 1) * stat_all[i];
y = step * num_mol;
p = x / y;
pn = (i + 1) * p;
fprintf (f_out, " %7i %7i %9.2f %9.5f %10.5f\n", i+1, stat_all[i], conc, p, pn);
}
fprintf (f_out, "------------------------------------------------\n");
if (max_depth > 0)
{
// types of agglomerates
// linear and cycle
x = type_agl[0] + type_agl[1];
type[0] = type_agl[0];
type[1] = type_agl[1];
fprintf (f_out, "LINEAR=%.5f\nCYCLE=%.5f\n--------------------\n", type[0]/x, type[1]/x);
// branched
type[0] = type_agl[2];
type[1] = type_agl[3];
fprintf (f_out, "NOT BRANCHED=%.5f\nBRANCHED=%.5f\n--------------------\n", type[0]/x, type[1]/x);
// n_cycle
x = 0;
for (i=4; i<max_depth+2; i++)
x += type_agl[i];
for (i=4; i<max_depth+2; i++)
{
type[0] = type_agl[i];
fprintf (f_out, "CYCLE_'%2i'=%.5f\n", i-1, type[0]/x);
}
}
fclose (f_out);
return 0;
}