atomes 1.1.14
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 |
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 | Write XYZ atomic coordinates |
► 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-b.c | |
main.c | Initialization of the atomes program Functions required to read data from the command line |
msdcall.c | Callbacks for the MSD calculation dialog |
ringscall.c | Callbacks for the ring statistics 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_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 |
► 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 |