diff --git a/mathmech/PKGBUILD b/mathmech/PKGBUILD new file mode 100644 index 0000000..eccbd7c --- /dev/null +++ b/mathmech/PKGBUILD @@ -0,0 +1,32 @@ +# Author: Evgeniy "arcanis" Alexeev +# Maintainer: Evgeniy "arcanis" Alexeev + +pkgname=mathmech +pkgver=1.0.1 +pkgrel=1 +pkgdesc="Software package for analysis of molecular dynamics trajectories" +arch=(any) +url="https://github.com/arcan1s/moldyn/mathmech" +license=('GPL') +depends=('qt4' 'qwt') +makedepends=('unzip' 'cmake' 'automoc4') +source=(https://github.com/arcan1s/moldyn/releases/download/mm-1.0.1/${pkgname}-${pkgver}.zip) +md5sums=('5fab4bc7707d580ff41d384b1875b32c') + +build () +{ + unzip -o -q ${srcdir}/${pkgname}-${pkgver}.zip -d ${srcdir}/${pkgname} + if [ -d ${srcdir}/${pkgname}/build ]; then + rm -rf build + fi + mkdir ${srcdir}/${pkgname}/build && cd ${srcdir}/${pkgname}/build + cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../ + make +} + +package() +{ + cd ${srcdir}/${pkgname}/build + make DESTDIR=${pkgdir} install +} + diff --git a/mathmech/mathmech-1.0.1.zip b/mathmech/mathmech-1.0.1.zip new file mode 100644 index 0000000..a4b9601 Binary files /dev/null and b/mathmech/mathmech-1.0.1.zip differ diff --git a/mathmech/mathmech/bin/mm_agl b/mathmech/mathmech/bin/mm_agl deleted file mode 100755 index 856b7ba..0000000 Binary files a/mathmech/mathmech/bin/mm_agl and /dev/null differ diff --git a/mathmech/mathmech/bin/mm_envir b/mathmech/mathmech/bin/mm_envir deleted file mode 100755 index 8de9f79..0000000 Binary files a/mathmech/mathmech/bin/mm_envir and /dev/null differ diff --git a/mathmech/mathmech/bin/mm_radf b/mathmech/mathmech/bin/mm_radf deleted file mode 100755 index 91dfddc..0000000 Binary files a/mathmech/mathmech/bin/mm_radf and /dev/null differ diff --git a/mathmech/mathmech/bin/mm_statgen b/mathmech/mathmech/bin/mm_statgen deleted file mode 100755 index 0ed5810..0000000 Binary files a/mathmech/mathmech/bin/mm_statgen and /dev/null differ diff --git a/mathmech/mathmech/bin/mm_trj b/mathmech/mathmech/bin/mm_trj deleted file mode 100755 index 5d7f231..0000000 Binary files a/mathmech/mathmech/bin/mm_trj and /dev/null differ diff --git a/mathmech/mathmech/bin/mm_trj2pdb b/mathmech/mathmech/bin/mm_trj2pdb deleted file mode 100755 index d040b8b..0000000 Binary files a/mathmech/mathmech/bin/mm_trj2pdb and /dev/null differ diff --git a/mathmech/mathmech/logo.png b/mathmech/mathmech/mathmech-logo.png similarity index 100% rename from mathmech/mathmech/logo.png rename to mathmech/mathmech/mathmech-logo.png diff --git a/mathmech/mathmech/mathmech.desktop b/mathmech/mathmech/mathmech.desktop new file mode 100644 index 0000000..afcfd02 --- /dev/null +++ b/mathmech/mathmech/mathmech.desktop @@ -0,0 +1,9 @@ +[Desktop Entry] +Name=Mathematical Molecular Mechanics +Comment=GUI for mathmech program pack +Exec=mathmech +Icon=mathmech-logo +Terminal=false +Encoding=UTF-8 +Type=Application +Categories=Qt;Science;Chemistry;Physics;Education; diff --git a/mathmech/mathmech/resources/translations/eng.qm b/mathmech/mathmech/resources/translations/eng.qm deleted file mode 100644 index d843fd1..0000000 Binary files a/mathmech/mathmech/resources/translations/eng.qm and /dev/null differ diff --git a/mathmech/mathmech/resources/translations/eng.ts b/mathmech/mathmech/resources/translations/eng.ts index 1507361..e44e3ae 100644 --- a/mathmech/mathmech/resources/translations/eng.ts +++ b/mathmech/mathmech/resources/translations/eng.ts @@ -383,562 +383,564 @@ p, li { white-space: pre-wrap; } Ready - - - - - + + + + + Select work directory Select work directory - - - + + + Select trajectory file Select trajectory file - + All files (*.*) All files (*.*) - + Select atom types file Select atom types file - + Atom types files (*.types);;All files (*.*) Atom types files (*.types);;All files (*.*) - + Save files as Save files as - + Mask of trajectory files Mask of trajectory files - - - - - + + + + + Save log file as... Save log file as... - - - - - + + + + + Log files (*.log) Log files (*.log) - - + + Select trajectory files Select trajectory files - - - - + + + + Trajectory files (*.*[0-9]) Trajectory files (*.*[0-9]) - - + + Save output file as... Save output file as... - - + + Output files (*.dat) Output files (*.dat) - - + + Save PDB file as... Save PDB file as... - - + + PDB files (*.pdb) PDB files (*.pdb) - + Select agglomerate file Select agglomerate file - + Agglomerate files (*.agl);;All files (*.*) Agglomerate files (*.agl);;All files (*.*) - - + + Processing 'trj'... Processing 'trj'... - - - - - + + + + + Done Done - - + + Processing 'statgen'... Processing 'statgen'... - - + + Processing 'envir'... Processing 'envir'... - - + + Processing 'radf'... Processing 'radf'... - - + + Processing 'agl'... Processing 'agl'... - - + + Processing 'trj2pdb'... Processing 'trj2pdb'... - + Mathematical Molecular Mechanics Mathematical Molecular Mechanics - + &Quit &Quit - + Quit Quit - + Ctrl+Q Ctrl+Q - &Help - &Help + &Help - F1 - F1 + F1 - + About About - + Atom &types file Atom &types file - + &Agglomerate file &Agglomerate file - + &Settings &Settings - + + Ctrl+P + Ctrl+P + + + agl_all agl_all - statgen_all - statgen_all + statgen_all - - - - - + + + + + Work directory Work directory - - - - + + + - - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + Browse Browse - - - + + + Input file Input file - + Type of trajectory Type of trajectory - + GROMACS text GROMACS text - + PUMA PUMA - + Number of steps Number of steps - + Atom type file Atom type file - + Mask of output files Mask of output files - + Total atom types Total atom types - - - - - + + + + + Log Log - - - - - + + + + + Clear Clear - - - - - + + + + + Start Start - + Generate trajectory Generate trajectory - - + + Mask of input files Mask of input files - - + + Steps Steps - - + + first first - - + + last last - - - - - - Cell, A - Cell, A - - - - - - - X - X - - - - - - - Y - Y - + Cell, A + Cell, A + + + + + + + X + X + + + + + + + Y + Y + + + + + + Z Z - + atom 0 atom 0 - - + + atom 1 atom 1 - - + + atom 2 atom 2 - - + + atom 3 atom 3 - + Interaction Interaction - + 0-0 0-0 - + Save Save - + Add Add - + Remove Remove - - - - + + + + Output file Output file - + Depth of search Depth of search - + Analysis Analysis - - + + Graph Graph - + Agglomeration Agglomeration - + Molecule Molecule - + Radius Radius - + Environment Environment - + One atom function One atom function - + Three atom function Three atom function - + R, A R, A - - + + min min - - + + max max - - + + step step - + Angle, deg Angle, deg - + Matrix Matrix - + RADF RADF - + From agglomerate - + From trajectory snapshot From trajectory snapshot - + File with agglomerate File with agglomerate - + Generate PDB Generate PDB - + Menu Menu - + File &creator File &creator - + &Tools &Tools - + Help Help @@ -966,72 +968,72 @@ p, li { white-space: pre-wrap; } All files (*) - + Settings Settings - + mm_trj mm_trj - - - - - - + + + + + + Browse Browse - + mm_statgen mm_statgen - + mm_envir mm_envir - + mm_radf mm_radf - + mm_trj2pdb mm_trj2pdb - + mm_agl mm_agl - + English English - + Russian Russian - + You need to restart application You need to restart application - + Save Save - + Close Close diff --git a/mathmech/mathmech/resources/translations/rus.qm b/mathmech/mathmech/resources/translations/rus.qm deleted file mode 100644 index 086f2fb..0000000 Binary files a/mathmech/mathmech/resources/translations/rus.qm and /dev/null differ diff --git a/mathmech/mathmech/resources/translations/rus.ts b/mathmech/mathmech/resources/translations/rus.ts index d925965..6c47959 100644 --- a/mathmech/mathmech/resources/translations/rus.ts +++ b/mathmech/mathmech/resources/translations/rus.ts @@ -383,564 +383,566 @@ p, li { white-space: pre-wrap; } Готов - - - - - + + + + + Select work directory Выбор рабочей директории - - - + + + Select trajectory file Выбор файла траектории - + All files (*.*) Все файлы (*.*) - + Select atom types file Выбор файла типов атомов - + Atom types files (*.types);;All files (*.*) Файл типов атомов (*.types);;Все файлы (*.*) - + Save files as Сохранить файл как... - + Mask of trajectory files Маска файлов траектории - - - - - + + + + + Save log file as... Сохранить лог как... - - - - - + + + + + Log files (*.log) Лог (*.log) - - + + Select trajectory files Выбор файла траектории - - - - + + + + Trajectory files (*.*[0-9]) Файлы траектории (*.*[0-9]) - - + + Save output file as... Сохранить файл как... - - + + Output files (*.dat) Выходной файл (*.dat) - - + + Save PDB file as... Сохранить PDB как... - - + + PDB files (*.pdb) PDB файл (*.pdb) - + Select agglomerate file Выбор файла с агломератом - + Agglomerate files (*.agl);;All files (*.*) Файл с агломератом (*.agl);Все файлы (*.*) - - + + Processing 'trj'... Выполняется 'trj'... - - - - - + + + + + Done Готово - - + + Processing 'statgen'... Выполняется 'statgen'... - - + + Processing 'envir'... Выполняется 'envir'... - - + + Processing 'radf'... Выполняется 'radf'... - - + + Processing 'agl'... Выполняется 'agl'... - - + + Processing 'trj2pdb'... Выполняется 'trj2pdb'... - + Mathematical Molecular Mechanics Mathematical Molecular Mechanics - + Generate trajectory Создать траекторию - - - - - + + + + + Work directory Рабочая директория - - - - + + + - - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + Browse Обзор - - - + + + Input file Входной файл - + Type of trajectory Тип траектории - + GROMACS text GROMACS - + PUMA PUMA - + Number of steps Число шагов - + Atom type file Файл типов атомов - + Mask of output files Маска файлов - + Total atom types Всего типов атомов - - - - - + + + + + Log Лог - - - - - + + + + + Clear Очистить - - - - - + + + + + Start Старт - + Agglomeration Агломерация - - + + Mask of input files Маска файлов - - + + Ctrl+P + Ctrl+P + + + + Steps Шаги - - + + first первый - - + + last последний - - - - - - Cell, A - Ячейка, А - - - - - - - X - X - - - - - - - Y - Y - + Cell, A + Ячейка, А + + + + + + + X + X + + + + + + + Y + Y + + + + + + Z Z - + atom 0 атом 0 - - + + atom 1 атом 1 - - + + atom 2 атом 2 - - + + atom 3 атом 3 - + Interaction Взаимодействие - + 0-0 0-0 - + Save Сохранить - + Add Добавить - + Remove Удалить - - - - + + + + Output file Выходной файл - + Depth of search Глубина поиска - + Analysis Анализ - - + + Graph График - + Environment Окружение - + Molecule Молекула - + Radius Радиус - + RADF ФРУР - + One atom function Одноатомная функция - + Three atom function Трехатомная функция - + R, A R, A - - + + min min - - + + max max - - + + step шаг - + Angle, deg Угол, град - + Matrix Матрица - + Generate PDB Создать PDB - + From agglomerate Из агломерата - + From trajectory snapshot Из снимка траектории - + File with agglomerate Файл с агломератом - + Menu Меню - + File &creator &Создание файлов - + &Tools &Утилиты - + Help Помощь - + &Quit &Выход - + Quit Выход - + Ctrl+Q Ctrl+Q - &Help - &Помощь + &Помощь - F1 - F1 + F1 - + About О программе - + Atom &types file Файл типов &атомов - + &Agglomerate file Файл с &агломератом - + &Settings &Настройки - + agl_all agl_all - statgen_all - statgen_all + statgen_all @@ -966,72 +968,72 @@ p, li { white-space: pre-wrap; } Все файлы (*) - + Settings Настройки - + mm_trj mm_trj - - - - - - + + + + + + Browse Обзор - + mm_statgen mm_statgen - + mm_envir mm_envir - + mm_radf mm_radf - + mm_trj2pdb mm_trj2pdb - + mm_agl mm_agl - + English English - + Russian Russian - + You need to restart application You need to restart application - + Save Сохранить - + Close Закрыть diff --git a/mathmech/mathmech/src/CMakeLists.txt b/mathmech/mathmech/src/CMakeLists.txt index 44daab0..626b9d8 100644 --- a/mathmech/mathmech/src/CMakeLists.txt +++ b/mathmech/mathmech/src/CMakeLists.txt @@ -46,7 +46,7 @@ foreach (LANGUAGE ${LANGUAGES}) OUTPUT ${QM} COMMAND ${QT_LRELEASE_EXECUTABLE} ${TS} MAIN_DEPENDENCY ${TS}) -endforeach() +endforeach () add_custom_target ( translations COMMAND ${QT_LUPDATE_EXECUTABLE} ${HEADERS} ${SOURCES} ${UI_HEADERS} -ts ${TRANSLATIONS}) @@ -65,4 +65,8 @@ add_executable (${PROJECT} WIN32 ${UI_HEADERS} ${HEADERS} ${SOURCES} ${MOC_SOURC target_link_libraries (${PROJECT} ${LIBRARIES} ${QT_LIBRARIES} ${QT_QTMAIN_LIBRARY}) # install properties -INSTALL (TARGETS ${PROJECT} DESTINATION bin) +install (TARGETS ${PROJECT} DESTINATION bin) +install (FILES ../mathmech.desktop + DESTINATION share/applications/) +install (FILES ../mathmech-logo.png + DESTINATION share/pixmaps/) diff --git a/mathmech/mathmech/src/mainwindow.cpp b/mathmech/mathmech/src/mainwindow.cpp index d01150e..9ec62e2 100644 --- a/mathmech/mathmech/src/mainwindow.cpp +++ b/mathmech/mathmech/src/mainwindow.cpp @@ -123,9 +123,19 @@ void MainWindow::on_statgen_checkBox_atoms3_stateChanged(int arg1) void MainWindow::on_statgen_checkBox_anal_stateChanged(int arg1) { if (arg1 == 0) + { ui->statgen_doubleSpinBox_anal->setDisabled(true); + ui->statgen_spinBox_anal->setDisabled(true); + ui->statgen_checkBox_graph->setCheckState(Qt::Checked); + ui->statgen_checkBox_graph->setEnabled(true); + } else if (arg1 == 2) + { ui->statgen_doubleSpinBox_anal->setEnabled(true); + ui->statgen_spinBox_anal->setEnabled(true); + ui->statgen_checkBox_graph->setCheckState(Qt::Unchecked); + ui->statgen_checkBox_graph->setDisabled(true); + } } void MainWindow::on_envir_checkBox_log_stateChanged(int arg1) @@ -664,8 +674,12 @@ void MainWindow::start_events_statgen() else depth = QString("#"); float int_step; + int imax; if (ui->statgen_checkBox_anal->checkState() == 2) + { int_step = ui->statgen_doubleSpinBox_anal->value(); + imax = ui->statgen_spinBox_anal->value(); + } QString log; if (ui->statgen_checkBox_log->checkState() == 2) log = ui->statgen_lineEdit_log->text(); @@ -699,7 +713,7 @@ void MainWindow::start_events_statgen() output, depth, log, - int_step); + int_step, imax); ui->statusBar->showMessage(QApplication::translate("MainWindow", "Done")); if ((ui->statgen_checkBox_graph->checkState() == 2) && (check == true)) diff --git a/mathmech/mathmech/src/mainwindow.ui b/mathmech/mathmech/src/mainwindow.ui index ca84cd9..c824175 100644 --- a/mathmech/mathmech/src/mainwindow.ui +++ b/mathmech/mathmech/src/mainwindow.ui @@ -1245,6 +1245,25 @@ + + + + false + + + + 80 + 23 + + + + 1 + + + 10 + + + @@ -3467,14 +3486,6 @@ Ctrl+Q - - - &Help - - - F1 - - About @@ -3494,17 +3505,15 @@ &Settings + + Ctrl+P + agl_all - - - statgen_all - - @@ -3556,6 +3565,7 @@ statgen_pushButton_log statgen_checkBox_anal statgen_doubleSpinBox_anal + statgen_spinBox_anal statgen_checkBox_graph statgen_pushButton_clear statgen_pushButton_start diff --git a/mathmech/mathmech/src/mathmech.pro.user b/mathmech/mathmech/src/mathmech.pro.user index afa1552..de41466 100644 --- a/mathmech/mathmech/src/mathmech.pro.user +++ b/mathmech/mathmech/src/mathmech.pro.user @@ -1,6 +1,6 @@ - + ProjectExplorer.Project.ActiveTarget diff --git a/mathmech/mathmech/src/settingswindow.cpp b/mathmech/mathmech/src/settingswindow.cpp index a2ebdb4..a0e1094 100644 --- a/mathmech/mathmech/src/settingswindow.cpp +++ b/mathmech/mathmech/src/settingswindow.cpp @@ -30,7 +30,7 @@ SettingsWindow::SettingsWindow(MainWindow *parent) : else { setDefaults(); - applySettings(); + printSettings(); } showSettings(); ui->settings_layout_lang_2->setHidden(true); @@ -117,12 +117,12 @@ void SettingsWindow::setDefaults() suffix = QString(".exe"); #endif _parent->language = QString("eng"); - _parent->mm_trj_path = QDir::currentPath() + QDir::separator() + "mm_trj" + suffix; - _parent->mm_statgen_path = QDir::currentPath() + QDir::separator() + "mm_statgen" + suffix; - _parent->mm_envir_path = QDir::currentPath() + QDir::separator() + "mm_envir" + suffix; - _parent->mm_radf_path = QDir::currentPath() + QDir::separator() + "mm_radf" + suffix; - _parent->mm_trj2pdb_path = QDir::currentPath() + QDir::separator() + "mm_trj2pdb" + suffix; - _parent->mm_agl_path = QDir::currentPath() + QDir::separator() + "mm_agl" + suffix; + _parent->mm_trj_path = qApp->applicationDirPath() + QDir::separator() + "mm_trj" + suffix; + _parent->mm_statgen_path = qApp->applicationDirPath() + QDir::separator() + "mm_statgen" + suffix; + _parent->mm_envir_path = qApp->applicationDirPath() + QDir::separator() + "mm_envir" + suffix; + _parent->mm_radf_path = qApp->applicationDirPath() + QDir::separator() + "mm_radf" + suffix; + _parent->mm_trj2pdb_path = qApp->applicationDirPath() + QDir::separator() + "mm_trj2pdb" + suffix; + _parent->mm_agl_path = qApp->applicationDirPath() + QDir::separator() + "mm_agl" + suffix; } void SettingsWindow::readSettings() diff --git a/mathmech/mathmech/src/start_events.cpp b/mathmech/mathmech/src/start_events.cpp index 0e3f33d..2d4af11 100644 --- a/mathmech/mathmech/src/start_events.cpp +++ b/mathmech/mathmech/src/start_events.cpp @@ -1,4 +1,5 @@ #include +#include #include "mainwindow.h" #include "ui_mainwindow.h" @@ -189,7 +190,7 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path, QString output, QString depth, QString log, - float int_step) + float int_step, int imax) { // error check errorwin = new ErrorWindow(parent); @@ -238,12 +239,11 @@ bool Start_events::start_statgen_analysis(QString mm_statgen_path, delete errorwin; // parsing criteria - int imax = 10; QStringList inter_list = inter.split(QString(" -r "), QString::SkipEmptyParts); float *inter_list_one; inter_list_one = new float[16*inter_list.count()]; for (int i=0; i<16*inter_list.count(); i++) - inter_list_one[i] = -1.0; + inter_list_one[i] = 0.0; float item; int index; for (int i=0; i inter_list_index; for (int i=0; i<16*inter_list.count(); i++) - if (inter_list_one[i] > 0.0) - while (imax*int_step > inter_list_one[i]) - imax--; + if (inter_list_one[i] != 0.0) + inter_list_index.append(i); + int files = pow(2*imax+1, inter_list_index.count()); // exec - for (int i=-imax; i<=imax; i++) + char file[32]; + int first, second, step; + float *cur_inter; + cur_inter = new float[16*inter_list.count()]; + QString one_inter; + for (int i=0; i<16*inter_list.count(); i++) + cur_inter[i] = 0.0; + for (int i=0; iAbout this program: *
    - *
  • Program that creates PDB file with chosen aglomerate + *
  • Program that creates PDB file with chosen agglomerate *
* * Developer: @@ -27,7 +27,7 @@ * mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ] * * Parametrs: - * -a - input file with aglomerates (in format statgen) + * -a - input file with agglomerates (in format statgen) * -i - input file with coordinates * -c - cell size (float), A * -o - output file name @@ -100,7 +100,7 @@ int main(int argc, char *argv[]) int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet, *true_label_mol; -/* aglinp aglomerate file name +/* aglinp agglomerate file name * ch_type_atoms massive of char atom types * input input file name * logfile log file name @@ -127,14 +127,14 @@ int main(int argc, char *argv[]) if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0')) { sprintf (tmp_str, " mm_agl\n"); - sprintf (tmp_str, "%sProgram for create PDB file with chosen aglomerate\n", tmp_str); + sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\n", tmp_str); sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str); sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str); sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str); sprintf (tmp_str, "%sUsage:\n", tmp_str); sprintf (tmp_str, "%smm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str); sprintf (tmp_str, "%sParametrs:\n", tmp_str); - sprintf (tmp_str, "%s -a - input file with aglomerates (in format statgen)\n", tmp_str); + sprintf (tmp_str, "%s -a - input file with agglomerates (in format statgen)\n", tmp_str); sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str); sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str); sprintf (tmp_str, "%s -o - output file name\n", tmp_str); @@ -238,13 +238,13 @@ int main(int argc, char *argv[]) print_message (quiet, stdout, log, f_log, 6, argv[0]); -// reading aglomerate +// reading agglomerate print_message (quiet, stdout, log, f_log, 7, aglinp); error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol); if (error == 0) { - sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", ' ', num_needed_mol); + sprintf (tmp_str, "%6cNumber of molecules in agglomerate: %i\n", ' ', num_needed_mol); print_message (quiet, stdout, log, f_log, 8, tmp_str); // reading coordinates print_message (quiet, stdout, log, f_log, 7, input); diff --git a/mathmech/mm_agl/src/messages.c b/mathmech/mm_agl/src/messages.c index b7b4b3c..140cea8 100644 --- a/mathmech/mm_agl/src/messages.c +++ b/mathmech/mm_agl/src/messages.c @@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output) sprintf (out, "Initialization of variables from file '%s'\n", text); break; case 4: - sprintf (out, "%6cAglomerate was selected successfully\n", ' '); + sprintf (out, "%6cAgglomerate was selected successfully\n", ' '); break; case 5: sprintf (out, "Initial parametrs: \n%s", text); diff --git a/mathmech/mm_agl/src/read_agl.c b/mathmech/mm_agl/src/read_agl.c index d1754d9..239a453 100644 --- a/mathmech/mm_agl/src/read_agl.c +++ b/mathmech/mm_agl/src/read_agl.c @@ -1,7 +1,7 @@ /** * @file */ -/* Library for reading aglomerate from statgen-file +/* Library for reading agglomerate from statgen-file * * Usage: * reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol) @@ -15,14 +15,14 @@ */ int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol) /** - * @brief function that reads aglomerate from statgen-formated file + * @brief function that reads agglomerate from statgen-formated file * @code * reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol); * @endcode * - * @param aglinp aglomerate file name + * @param aglinp agglomerate file name * @param num_needed_mol number of needed molecules - * @param agl_class aglomerate class + * @param agl_class agglomerate class * @param needed_mol massive of numbed of needed molecules * * @return 0 - exit without errors @@ -33,7 +33,7 @@ int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int * FILE *f_agl; /* connect - connectivity matrix for molecule - * f_agl - aglomerate file + * f_agl - agglomerate file */ f_agl = fopen (aglinp, "r"); diff --git a/mathmech/mm_envir/src/messages.c b/mathmech/mm_envir/src/messages.c index b7b4b3c..140cea8 100644 --- a/mathmech/mm_envir/src/messages.c +++ b/mathmech/mm_envir/src/messages.c @@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output) sprintf (out, "Initialization of variables from file '%s'\n", text); break; case 4: - sprintf (out, "%6cAglomerate was selected successfully\n", ' '); + sprintf (out, "%6cAgglomerate was selected successfully\n", ' '); break; case 5: sprintf (out, "Initial parametrs: \n%s", text); diff --git a/mathmech/mm_radf/src/messages.c b/mathmech/mm_radf/src/messages.c index b7b4b3c..140cea8 100644 --- a/mathmech/mm_radf/src/messages.c +++ b/mathmech/mm_radf/src/messages.c @@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output) sprintf (out, "Initialization of variables from file '%s'\n", text); break; case 4: - sprintf (out, "%6cAglomerate was selected successfully\n", ' '); + sprintf (out, "%6cAgglomerate was selected successfully\n", ' '); break; case 5: sprintf (out, "Initial parametrs: \n%s", text); diff --git a/mathmech/mm_statgen/mm_statgen.pdf b/mathmech/mm_statgen/mm_statgen.pdf index 543c1ae..ddd19c1 100644 Binary files a/mathmech/mm_statgen/mm_statgen.pdf and b/mathmech/mm_statgen/mm_statgen.pdf differ diff --git a/mathmech/mm_statgen/src/main.c b/mathmech/mm_statgen/src/main.c index 4381892..e8b1270 100644 --- a/mathmech/mm_statgen/src/main.c +++ b/mathmech/mm_statgen/src/main.c @@ -116,7 +116,7 @@ int main (int argc, char *argv[]) * coords massive of coordinates * crit massive of criteria * - * agl massive of aglomerates + * agl massive of agglomerates * connect connectivity graph for all molecules * from first trajectory step * label_atom massive of atom types for interactions @@ -125,14 +125,14 @@ int main (int argc, char *argv[]) * 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_mol_agl massive of number of molecules in agglomerates * 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_agl massive of number of agglomerate types * type_atoms massive of atom types * type_inter number of atoms for interactions * quiet status of quiet-mode diff --git a/mathmech/mm_statgen/src/messages.c b/mathmech/mm_statgen/src/messages.c index b7b4b3c..140cea8 100644 --- a/mathmech/mm_statgen/src/messages.c +++ b/mathmech/mm_statgen/src/messages.c @@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output) sprintf (out, "Initialization of variables from file '%s'\n", text); break; case 4: - sprintf (out, "%6cAglomerate was selected successfully\n", ' '); + sprintf (out, "%6cAgglomerate was selected successfully\n", ' '); break; case 5: sprintf (out, "Initial parametrs: \n%s", text); diff --git a/mathmech/mm_statgen/src/stat_print.c b/mathmech/mm_statgen/src/stat_print.c index b69817a..9193332 100644 --- a/mathmech/mm_statgen/src/stat_print.c +++ b/mathmech/mm_statgen/src/stat_print.c @@ -15,11 +15,11 @@ 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 aglomerates to output file + * @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_aglomerates, aglomerates, statistic, max_depth, - * type_of_aglomerate); + * num_of_molecules_in_agglomerates, agglomerates, statistic, max_depth, + * type_of_agglomerate); * @endcode * * @param input input file name @@ -27,11 +27,11 @@ int printing_agl (const char *input, const char *output, const int *connect, * @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 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 aglomerate types + * @param type_agl massive of number of agglomerate types * * @return 1 - memory error * @return 0 - exit without errors @@ -90,7 +90,7 @@ int printing_agl (const char *input, const char *output, const int *connect, if (error > 0) return 1; -// print class of aglomerate +// print class of agglomerate fprintf (f_out, "AGL=%i=", num_mol_agl[i]); for (j=0; j 0) { -// types of aglomerates +// types of agglomerates // linear and cycle x = type_agl[0] + type_agl[1]; type[0] = type_agl[0]; diff --git a/mathmech/mm_trj/src/messages.c b/mathmech/mm_trj/src/messages.c index b7b4b3c..140cea8 100644 --- a/mathmech/mm_trj/src/messages.c +++ b/mathmech/mm_trj/src/messages.c @@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output) sprintf (out, "Initialization of variables from file '%s'\n", text); break; case 4: - sprintf (out, "%6cAglomerate was selected successfully\n", ' '); + sprintf (out, "%6cAgglomerate was selected successfully\n", ' '); break; case 5: sprintf (out, "Initial parametrs: \n%s", text); diff --git a/mathmech/mm_trj2pdb/src/messages.c b/mathmech/mm_trj2pdb/src/messages.c index b7b4b3c..140cea8 100644 --- a/mathmech/mm_trj2pdb/src/messages.c +++ b/mathmech/mm_trj2pdb/src/messages.c @@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output) sprintf (out, "Initialization of variables from file '%s'\n", text); break; case 4: - sprintf (out, "%6cAglomerate was selected successfully\n", ' '); + sprintf (out, "%6cAgglomerate was selected successfully\n", ' '); break; case 5: sprintf (out, "Initial parametrs: \n%s", text);