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atomes 1.3.1
atomes: an atomic scale modeling tool box
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atomes 1.3.1
atomes: an atomic scale modeling tool box
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| calc | |
| cp2k | |
| cp2k.h | Variable declarations for the creation of the CP2K input file(s) |
| cp2k_basis.c | CP2K basis set, as delivered with CP2K v9.1 |
| cp2k_files.c | Functions to handle CP2K basis sets and pseudopotentials |
| cp2k_gth-basis.c | CP2K GTH basis set, as delivered with CP2K v9.1 |
| cp2k_init.c | Initialization of the CP2K input assistant |
| cp2k_mol.c | Functions to fix fragment(s) when creating the CP2K input file |
| cp2k_molopt-basis.c | CP2K MOLOPT basis set, as distributed with CP2K 9.1 |
| cp2k_pot.c | CP2K potentials, as distributed with CP2K v9.1 |
| cp2k_print.c | Functions to print the CP2K input file(s) |
| cpmd | |
| cpmd.h | Variable declarations for the creation of the CPMD input file |
| cpmd_atoms.c | Functions to handle dummy atom(s) for the CPMD input file |
| cpmd_init.c | Functions to initialize the QM / QM-MM input file creation assistant |
| cpmd_nose.c | Functions to prepare the thermostat(s) configuration widgets for QM / QM-MM input files |
| cpmd_print.c | Functions to print the CPMD input file(s) |
| cpmd_restart.c | Functions to configure the restart section for the CPMD input file creation assistant |
| dl_poly | |
| dlp_active.c | Functions to retrieve data in the force field structure |
| dlp_atom.c | Functions to handle atom selection(s) when creating a force field Functions to remove / add field atom from a force field |
| dlp_comp.c | Functions to compare and adjust field body parameters |
| dlp_control.c | Functions to handle the creation of the DL-POLY CONTROL file |
| dlp_copy.c | Functions to copy force field and related data structures |
| dlp_edit.c | Functions to edit DL-POLY force field parameters |
| dlp_ff_match.c | Functions the list the available database parameters for the atom database window |
| dlp_field.c | Functions to prepare the DL-POLY / LAMMPS input preparation assistant Functions to design a classical force field |
| dlp_field.h | Variable declarations for the creation of the DL_POLY input file(s) |
| dlp_init.c | Functions to initialize the creation of a classical force field |
| dlp_mol.c | Functions to add / remove molecule(s) to / from the force field |
| dlp_print.c | Functions to handle the output of the DL-POLY FIELD file Functions to handle the output of the DL-POLY CONTROL file Functions to handle the output of the DL-POLY CONFIG file Functions to fill the structural element(s) tree models in the assistant |
| dlp_viz.c | Functions to handle the visualization events when creating a classical force field |
| force_fields | |
| force_fields.c | Functions to prepare the force field XML files from the sources in atomes Functions to read the force field XML files |
| force_fields.h | Variable declarations for the creation of the force field database |
| lammps | |
| la_print.c | Functions to print the LAMMPS input file(s) |
| calc.c | Callbacks used in by the molecular dynamics calculation assistants Atom selection structure manipulation tools The initialization of the assistants |
| calc.h | Variable declarations for the MD input preparation assistants |
| curve | |
| cedit.c | Initialization of the curve layout edition dialog |
| cedit.h | Variable declarations for the curve layout edition window |
| curve.c | Functions to manage curves |
| curve.h | Variable declarations for the curve widget Functions for interactions with the curve widget |
| cwidget.c | Initialization of the curve widget |
| datab.c | Curve data edition window and associated callbacks |
| datab.h | Variable declarations for the curve data edition window |
| draw.c | Function to draw a curve |
| frame.c | Functions to draw the frame |
| glyph.c | Functions to draw the glyphs |
| labels.c | Function to draw the axis labels |
| legend.c | Function to draw the legend |
| m_curve.c | Curve context menu (mouse right click) |
| show.c | Functions to draw the complete graph |
| tab-1.c | 1st tab of the curve layout edition dialog |
| tab-2.c | 2nd tab of the curve layout edition dialog |
| tab-3.c | 3rd tab of the curve layout edition dialog |
| tab-4.c | 4th tab of the curve layout edition dialog |
| title.c | Functions to draw the title |
| w_curve.c | Functions to create the graph/curve window |
| w_data.c | Functions to export curve data |
| w_img.c | Functions to save screenshot from graph / curve(s) |
| xaxis.c | Functions to draw the x axis |
| yaxis.c | Functions to draw the y axis |
| fortran | |
| allocbonds.F90 | Memory allocation for bonding properties analysis |
| allochem.F90 | Memory allocation for chemistry buffers |
| allocmsd.F90 | Memory allocation for MSD analysis |
| angles.F90 | Distribution of bond angles and dihedrals |
| bonds.F90 | Bonding properties |
| c3d.F90 | Write Chem3D atomic coordinates |
| chains.F90 | Chain statistics |
| chains_ogl.F90 | Send chain statistics data to C for OpenGL rendering |
| chemistry.F90 | Basic chemistry analysis |
| clean.F90 | Clean up Fortran90 data |
| cqvf.F90 | Q vectors selection for the reciprocal calculation of the S(k) |
| dmtx.F90 | Distance matrix calculation |
| dvtb.F90 | Model expansion for algorithmic purposes |
| escs.F90 | Edge and Corner sharing tetrahedra analysis |
| fzbt.F90 | Partial structure factors: Faber-Ziman and Bathia-Thornton analysis |
| gr.F90 | G(r) analysis: direct real space calculation |
| grfft.F90 | G(r) analysis: Fourier transform calculation |
| initchains.F90 | Initialize chain statistics |
| initrings.F90 | Initialize ring statistics |
| lattice.F90 | Lattice properties |
| mendeleiev.F90 | Periodic table and diffraction data |
| molecules.F90 | Fragment(s) and molecule(s) analysis |
| msd.F90 | MSD analysis |
| parameters.F90 | Global variable declarations |
| pdb.F90 | Unused: read atomic coordinates in PDB format - old version |
| prepdata.F90 | First level analysis of atomic coordinates |
| resrings.F90 | Export results of ring and chain statistics to C |
| rings-guttman.F90 | Guttman ring statistics |
| rings-king.F90 | King ring statistics |
| rings-primitive.F90 | Primitive and strong ring statistics |
| rings_ogl.F90 | Send ring statistics data to C for OpenGL rendering |
| sk.F90 | S(k) analysis: direct reciprocal space calculation |
| skt.F90 | S(k,t) analysis: dynamic structure factor calculation |
| spherical.F90 | Spherical harmonics analysis |
| sq.F90 | S(q) analysis: Fourier transform calculation |
| threads.F90 | OpenMP utility functions |
| trj.F90 | Unused: read atomic coordinates in CPMD trajectory format - old version |
| utils.F90 | Global function declarations |
| vas.F90 | Unused: read atomic coordinates in VASP trajectory format - old version |
| writedata.F90 | Export curve data using data received from C |
| xyz.F90 | |
| gui | |
| bdcall.c | Callbacks for the bond properties calculation dialog |
| calc_menu.c | Creation of the calculation dialogs |
| callbacks.c | General callbacks Functions to open and close files |
| callbacks.h | Callback declarations for main window |
| chainscall.c | Callbacks for the chains statistics calculation dialog |
| edit_menu.c | Creation of the edition dialogs |
| grcall.c | Callbacks for the g(r)/g(k) calculation dialog |
| gtk-misc.c | GTK3/GTK4 utility subroutines, instead of having pre-processor flags everywhere in the code. Whenever I need to use a GTK function that changed between v3 and v4, I created an home made function declared in this file, and deal then here with the potential GTK versions issues |
| gui.c | GUI of the main window Menu elements of the workspace menu Creation of menu items, actions, used in the entire atomes software |
| initc.c | Curve data buffer initialization |
| interface.c | General messaging functions |
| interface.h | Messaging function declarations |
| main.c | Initialization of the atomes program Functions required to read data from the command line |
| msdcall.c | Callbacks for the MSD calculation dialog |
| preferences.c | Functions to create the 'User preferences' window |
| preferences.h | Preference variable declarations |
| ringscall.c | Callbacks for the ring statistics calculation dialog |
| sktcall.c | Callbacks for the dynamic structure factor S(k,t) calculation dialog |
| spcall.c | Callbacks for the spherical harmonics calculation dialog |
| sqcall.c | Callbacks for the s(q) / s(k) calculation dialog |
| tools.c | Callbacks for the toolbox dialog |
| work_menu.c | Workspace menu GTK3 version Callbacks for the workspace menu |
| opengl | |
| draw | |
| d_atoms.c | Nctions to prepare the OpenGL rendering atom(s) and clone(s) |
| d_axis.c | Functions to prepare the OpenGL rendering for the axis |
| d_background.c | Functions to prepare the OpenGL rendering for the gradient background |
| d_bonds.c | Functions to prepare the OpenGL rendering of bond(s) and clone bond(s) |
| d_box.c | Functions to prepare the OpenGL rendering for the box(es) Functions to prepare the OpenGL rendering for the slab(s) Functions to prepare the OpenGL rendering for the volume(s) |
| d_label.c | Functions to prepare the OpenGL rendering of the atomic label(s) |
| d_measures.c | Functions to prepare the OpenGL rendering of the measure(s) |
| d_poly.c | Functions to prepare the OpenGL rendering of coordination polyhedra |
| d_rings.c | Functions to prepare the OpenGL rendering of rings polyhedra |
| d_selection.c | Functions to prepare the OpenGL rendering of the selected: atom(s), clone(s), bond(s) and clone bond(s) Functions to prepare the unique color rendering for picking the atom(s) and bond(s) |
| image.c | Functions to render an image from the OpenGL window |
| movie.c | Functions to encode a movie / render an image from the OpenGL rendering |
| movie.h | Data structure declarations for movie encoding Function declarations for movie encoding |
| ogl_text.c | Functions to prepare OpenGL rendering for text |
| edit | |
| atom_action.c | Functions to apply the edition actions to the model |
| atom_coord.c | Functions to correct the coordination menus and the corresponding data pointers after edition |
| atom_edit.c | Functions to create the model edition window |
| atom_edit.h | Function declarations for the mode edition window |
| atom_geo.c | Functions to check for the appropriate atomic coordinations |
| atom_insert.c | Functions to insert bond(s) in a project |
| atom_move.c | Functions to move atom(s) and group of atom(s) Functions to move randomly atom(s) and group of atom(s) Functions to create the motion widgets of the model edition window |
| atom_object.c | Functions to create atomic objects |
| atom_remove.c | Functions to remove bond(s) from a project Function to prepare the passivation (removal followed by insertion) |
| atom_search.c | Functions to prepare the model edition 'search' tabs and the associated widgets |
| atom_species.c | Functions to look for new chemical species and modify the chemical information accordingly |
| cbuild_action.c | Functions to build a crystal using space group, crystallographic position(s) and object(s) to insert |
| cbuild_edit.c | Functions to create the crystal builder window |
| cbuild_edit.h | Function declarations for the crystal builder |
| cbuild_info.c | Functions to create the space group information dialog |
| cbuild_sg.c | Functions to read space group data from XML files |
| cell_cut.c | Functions to create the 'slab cutting' tab of the cell edition window |
| cell_density.c | Functions to create the 'density adjustment' tab in the cell edition window |
| cell_edit.c | Functions to create the cell edition window |
| cell_edit.h | Function declarations for the cell edition window |
| cell_extra.c | Functions to create the 'add cell(s)' tab in the cell edition window |
| cell_pixel.c | Functions to create the pixel debugging tab for the cell edition window This is only used when DEBUG option is activated at build time |
| cell_shift.c | Functions to create the 'shift cell center' tab for the cell edition window |
| cell_super.c | Functions to create a super-cell using the extra cell(s) |
| win | |
| color_box.c | Functions to create the color palettes for the menus of the OpenGL window Callbacks to set the color using the color palettes |
| color_box.h | Structure definitions for color management Function declarations for color management |
| glwindow.c | Functions to create a project OpenGL window |
| glwindow.h | Function declarations for the creation of the OpenGL window |
| initchain.c | Functions collecting chain(s) data from Fortran90 Functions allocating chain(s) data from Fortran90 |
| initcoord.c | Coordinations and polyhedra menus initialization Coordinations and polyhedra GTK3 menus and menu items creation Initialization of coordinations and polyhedra related data from Fortran90 information |
| initcoord.h | Function declarations to handle the atomic coordination data |
| initmol.c | Functions to retrieve fragments data from Fortran90 Functions to retrieve molecules data from Fortran90 Functions to analyze molecule topology |
| initring.c | Functions to retrieve rings data from Fortran90 |
| m_anim.c | Functions to create the 'Animate' submenu |
| m_atoms.c | Functions to create the 'Model -> Atom(s)' submenu |
| m_axis.c | Functions to create the 'View -> Axis' submenu |
| m_back.c | Function to create the background color menu item |
| m_bonds.c | Functions to create the 'Model -> Bond(s)' submenu |
| m_box.c | Functions to create the 'Model -> Box' submenu |
| m_clones.c | Functions to create the 'Model -> Clone(s)' submenu |
| m_coord.c | Functions to create the 'Chemistry -> Coordination' submenu |
| m_edit.c | Functions to create the 'Tools -> Edit' submenu |
| m_map.c | Functions to create the 'OpenGL -> Color Scheme(s)' submenus Functions to handle custom color maps |
| m_poly.c | Functions to create the 'Chemistry -> Polyhedra' submenus |
| m_proj.c | Functions to create the 'View -> Projection' submenu |
| m_quality.c | Functions to create the 'OengGL -> Quality' submenu |
| m_render.c | Functions to create the 'OpenGL -> Render' submenu |
| m_rep.c | Functions to create the 'View -> Representation' submenu |
| m_style.c | Functions to create the 'OpenGL -> Style' submenu |
| m_tools.c | Functions to create the 'Tools' submenu |
| menu_bar.c | Functions to create the menu bar of the OpenGL window Functions to create the menu items for the menu bar and the pop up menu |
| popup.c | Functions to create the OpenGL window popup menus: |
| submenus.h | Function declarations for the creation of the OpenGL window menus |
| w_advance.c | Functions to create the OpenGL parameters edition window |
| w_atoms.c | Functions to create the atom(s) / clone(s) advanced configuration window |
| w_axis.c | Functions to create the axis parameters edition window |
| w_bonds.c | Functions to create the bond (legnth/radius) edition window(s) |
| w_box.c | Functions to create the box properties window |
| w_chains.c | Functions to create the chain(s) tab for the advanced environments window |
| w_colors.c | Functions to create the color selection dialogs |
| w_coord.c | Functions to create the 'Environments configuration' window |
| w_cutoffs.c | Functions to create the bond cutoffs update dialog |
| w_encode.c | Functions to create the encoding (image/video) window |
| w_labels.c | Functions to create the 'atomic labels' tab of the atom(s) / clone(s) advanced configuration window Functions to create the measure labels window of the 'Measures' window |
| w_library.c | Functions to create the molecular library Functions to read the 'Simple chemical XML' files |
| w_measures.c | Functions to create the measurement(s) window |
| w_periodic.c | Functions to create the periodic table of the elements Functions to select element from the periodic table |
| w_record.c | Functions to create the recording window |
| w_rings.c | Functions to create the ring(s) tab for the advanced environments window |
| w_search.c | Functions to create the object search widgets, for: |
| w_sequencer.c | Functions to create the MD sequencer window |
| w_spiner.c | Functions to create the 'Spin' window |
| w_volumes.c | Functions to create the 'Volumes' window Functions to compute system / fragment / molecular volumes |
| arcball.c | Mouse trackball rotation functions |
| glview.c | Callbacks of the OpenGL window |
| glview.h | Variable declarations related to the OpenGL window Function declarations related to the OpenGL window |
| glwin.h | Variable declarations related the OpenGL window Data structure declarations related the OpenGL window |
| math_3d.h | Functions for OpenGL math |
| ogl_draw.c | OpenGL window drawing funcions |
| ogl_shaders.c | OpenGL shaders for the atomes program |
| ogl_shading.c | Functions to create GLSL programs Functions to manage GLSL programs |
| ogl_shading.h | Variable declarations related to GLSL programs Data structure declarations related to GLSL programs |
| ogl_utils.c | 2D and 3D calculations utilities for distances and angles |
| selection.c | Functions handling the atom and bond selection process in the OpenGL window |
| project | |
| readers | |
| read_c3d.c | Functions to read Chem3d atomic coordinates |
| read_cif.c | Functions to read CIF files |
| read_coord.c | General functions to import atomic coordinates |
| read_hist.c | Functions to read DL-POLY history file |
| read_isaacs.c | Functions to read an ISAACS XML file Functions to write an ISAACS XML file |
| read_isaacs.h | Function declarations to read / write ISAACS XML file |
| read_npt.c | Functions to read NPT data |
| read_pdb.c | Functions to read PDB files |
| read_trj.c | Functions to read CPMD atomic coordinates |
| read_vas.c | Functions to read VASP atomic coordinates |
| read_xyz.c | Functions to read XYZ atomic coordinates |
| readers.h | Functions declaration to read atomic coordinates |
| close_p.c | Functions to close an atomes project Callbacks to close an atomes project |
| debugio.c | Some debugging and printing functions |
| init_p.c | Functions to initialize an atomes project |
| open_p.c | Functions to start the reading of an atomes project file |
| project.c | Project management functions |
| project.h | Function declarations for reading atomes project file Function declarations for saving atomes project file |
| read_bond.c | Function to read bonding information in the atomes project file format |
| read_curve.c | Functions to read curve data in the atomes project file format |
| read_field.c | Functions to read DLPOLY force field data in the atomes project file format |
| read_mol.c | Functions to read molecule(s) data in the atomes project file format |
| read_opengl.c | Functions to read the OpenGL window data in the atomes project file format |
| read_qm.c | Functions to read ab-intio (CPMD/CP2K) calculation parameters in the atomes project file format |
| save_bond.c | Functions to save bonding information in the atomes project file format |
| save_curve.c | Functions to save curves information in the atomes project file format |
| save_field.c | Functions to save force field information in the atomes project file format |
| save_mol.c | Functions to save molecules information in the atomes project file format |
| save_opengl.c | Functions to save OpenGL information in the atomes project file format |
| save_p.c | Functions to start saving an atomes project file |
| save_qm.c | Functions to save ab-initio (CPMD/CP2K) calculation parameters in the atomes project file format |
| update_p.c | Functions to update a project Functions to activate a project |
| startup-testing | |
| startup_testing.c | Startup testing of OpenGL configuration for the atomes program |
| workspace | |
| modelinfo.c | Functions to display model information in GtkTextBuffer |
| workinfo.c | Functions to display project information in GtkTextBuffer |
| workspace.c | Implementation of the workspace tree view Associated callbacks |
| workspace.h | Function declarations for workspace managment |
| affero.h | The text of the Affero GPL v3 license |
| bind.h | Binding to the Fortran90 subroutines |
| config.h | |
| global.c | Global variables declaration Global convenience function implementations |
| global.h | Global variable declarations Global convenience function declarations Global data structure definitions |
1.16.1