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Aten v1.7 User Manual Last Updated Thursday, 21 July 2011

1. string source target source Engelbert target beforestr source e places the text Eng in the variable target string textl No taxes on axes string text2 beforestr textl ax places the text No taxes on in the variable text2 contains Syntax int contains string source string search Returns the number of times the search string is found in the source string The function counts only non overlapping occurrences of search For example 242 string poem six sixes are thirty six int count contains poem Six sets count to 3 ftoa Syntax string ftoa double d Converts the supplied double d into a string representation For example string num ftoa 100 001 would set num to the value 100 00 itoa Syntax string itoa int i Converts the supplied integer i into a string representation For example string num itoa 54 would set num to the value 54 lowercase Syntax string lowercase string source Returns the source string with all uppercase letters converted to lowercase replacechars Syntax string replacechars string source string searchchars string replacechar 243 Searches through the supplied source string and replaces all occurrences of the individual characters given in the string searchchars with the character supplied in replacechar returning the new string For example
2. Unnamed002 icy density Density 1 000000 Insertion Policy Partition 2 Slab _ Exact Number Specific Density _ Exact Number Density Relative Number Exact Density Population 0 Density 100000 glem3 M Allow component to be rotated Select multiple components with Shift and Ctrl Method Options lt Back Next gt Cancel lt Back Finish Cancel Finally model selection and preparation Select the water molecule from the list and press Next to get to the component setup page We must change the Target Partition of the water molecule to 2 the slab we defined earlier and then request that a Specific Density of molecules be inserted into this partition the default of 1 0 g cm is fine Once this information has been entered press Finish to start the build 31 A Aten vL7 11671 Unnamed001 lt lt no filename gt gt Modified Y Y Y File Edit View Selection Model Trajectory Forcefield Settings Scripts Help Jam SCY BHR e oag Lane Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle 1462 Atoms 18065 910000 g mol click drag or rotate in local frame right click drag ctrl remove from selection Orthorhombic 1 683752 g cm Script The script below creates the water molecule as the first step to make life a little easier newmodel Water newatom 0 addhydrogen s
3. exp Syntax double exp double x Returns the exponential of x In Syntax double ln double x Returns the natural base e logarithm of x log Syntax double log double x 197 Returns the base 10 logarithm of x nint Syntax int nint double x Returns the nearest integer value to x normalise Syntax double normalise vector v Normalises the vector v returning the magnitude of the vector before the normalisation was performed For example vector y lo 2 5 TP double mag normalise v printf Normalised vector is f Sf S mag was f n v x v y V Z mag prints the following Normalised vector is 0 267261 0 534522 0 801784 mag was 3 741657 random Syntax double random Return a random real number between 0 0 and 1 0 inclusive randomi Syntax int randomi int max RANDMAX Return a random integer between 0 and RANDMAX inclusive or 0 and max if it is supplied sin Syntax 198 double sin double angle Returns the sine of angle which should be given in degrees sqrt Syntax double sqrt double x Returns the square root of x tan Syntax double tan double angle Returns the tangent of angle which should be given in degrees 199 9 18 Measuring Commands Make measurements of distances angles and torsion angles dihedrals in models Note that there are two dis
4. moves the current selection 1 A along the x axis translateatom Syntax void translateatom double dx double dy double dz Translates the current atom by the specified vector For example translateatom 1 0 1 translates the current atom 1 A along x and 1 A along z translatecell Syntax void translatecell double fracx double fracy double fracz Translates the current selection by the fractional cell vectors specified The model must have a unit cell for this command to work For example translatecell 0 0 5 0 translates the current selection by an amount equivalent to half of the current cell s B vector 256 translateworld Syntax void translateworld double dx double dy double dz Translates the current selection by the A amounts specified with the XY plane parallel to the monitor screen For example translateworld 0 0 10 translates the current selection 10 A into the screen mirror Syntax void mirror string axis Mirror the current selection in the specified plane about its geometric centre For example MEROV mirrors the current selection about the y axis 257 9 32 View Commands Commands to change the current model s view axisrotateview Syntax void axisrotateview double ax double ay double az double angle Rotate the current view angle degrees about an axis defined between the supplied point ax a
5. requests that there will be 50 insertion attempts per cycle per molecule type printme Syntax void printmc Prints the current Monte Carlo parameters For example printmc 216 9 24 Pattern Commands Automatically or manually create pattern descriptions for models clearpatterns Syntax void clearpatterns Delete the pattern description of the current model It s a good idea to run this command before adding a pattern definition by hand with calls to newpattern For example clearpatterns createpatterns Syntax void createpatterns Automatically detect and create the pattern description for the current model For example createpatterns currentpattern Syntax pattern currentpattern pattern currentpattern string name pattern currentpattern int id Get the named pattern or pattern with given id if either was specified returning its reference and setting it to be the current pattern For example pattern p currentpattern liquid 217 sets the pattern named liquid in the current model to be the current pattern setting its reference in the variable p pattern p currentpattern returns a reference to the current pattern getpattern Syntax pattern getpattern string name pattern getpattern int id Get the named pattern or pattern with id specified returning its reference For example patter
6. string newstring replacechars Zero 2599 these numbers 123456789 0 replaces any numeric character with a zero replacestr Syntax string replacestr string source string searchstr string replacestr Replaces all occurrences of searchstr with replacestr in the supplied source string returning the result For example string fruity replacestr I don t like apples apples oranges would change your fondness towards apples removestr Syntax string removestr string source string searchstr Removes all occurrences of searchstr from the source string returning the result For example string debt removestr I owe you 2 million dollars million would reduce your outgoings considerably sprintf Syntax string sprintf string dest string format Prints a formatted string to the supplied variable dest and is an alias for the writevarf command 244 stripchars Syntax string stripchars string source string charlist Strip the supplied character s from the source string returning the result For example string abc stripchars Oodles of noodles o places the text Odles f ndles in the variable abc string abc abc Oodles of noodles abc stripchars abc aeiou strips all vowels from the input string placing the text Odls f ndl in the variable abc toa Syntax string toa string format R
7. Select by Description XXX Select by For Loop XXX 87 88 7 20 Trajectory Window If a trajectory is associated to the current model the trajectory toolbar allows to skip through frames and playback the trajectory Trajectory o x m IK lt gt DI Figure 7 34 Trajectory Window The E button serves to act as a toggle between displaying the actual trajectory frames and the parent model which owns those trajectory frames Its state is linked to the Trajectory View Model and Trajectory View Trajectory menu items of the main window and vice versa The set of standard playback controls allow individual frames to be skipped as well as going straight to the beginning or end of the trajectory The current frame may also be set with either the spin control or slider at the foot of the window The delay between swapping of frames is controlled by the slider on the right where the delay can be set in milliseconds Note that the actual speed of playback will also depend on the size of the system being viewed and the raw power of your graphics card 89 7 21 Transform Window For a selection of atoms rotational or matrix based transformations can be applied through the Transform Window Rotation About Arbitrary Axis Atom Transform o xX Axis Rotate Transform Matrix Convert Origin Axis Xx 0 00000 9 x 0 00000 0 Y 0 00000 Y 0 00000 o Z 0 00000 9 z 0 00000 S Define 22 Define 4 P
8. Syntax void flipz Flip negate the z coordinates of the current selection For example flipz matrixconvert Syntax void matrixconvert int i sx int j sx int 1 sy int j sy int i s2 int Jj 82 int i tx int J tx int 1 ty int 3 ty int i tz int j tz void matrixconvert int i sx int j sx int i sy int j sy int i Sz int J 82 int i tx int Jj tx ant i ty int j ty int 1 tz int j tz double oy double oz double oz void matrixconvert double s ax double s ay double s az double s bx double s by double s bz double s cx double s cy double s_Cz double t ax double t ay double t_az double t bx double t by double t bz double t_cx double t cy double t_cz void matrixconvert double s ax double s ay double s az double s bx double s by double s bz double s cx double s cy double s_Cz double t ax double t ay double t_az double t bx double t by double t bz double t cx double t cy double t_cz double oy double oz double oz From a defined frame of reference i e a set of axes defining the spatial orientation rotate the current selection from this frame into the second frame using the coordinate origin supplied or 0 0 0 by default In the first form six pairs of atom IDs define each matrix with the vectors taken to be 1 gt in all cases normalised to 1 0 and specifying the x y and z axes in turn In the second the matri
9. double elecenergy Calculates and returns the total electrostatic energy for the current model using the calculation method specified in the preferences expand Syntax void expand Expand the current atom selection along bonds See the expand command for more details finalise Syntax void finalise Finalise the current model See the finalisemodel command for more details interenergy Syntax double interenergy Calculates and returns the total intermolecular i e combined van der Waals and electrostatic energy for the current model intraenergy Syntax double intraenergy 117 Calculates and returns the total intramolecular i e combined bond angle and torsion energy for the current model movetoend Syntax void movetoend Move the current atom selection to the bottom highest IDs of the atom list See the movetoend command for more details movetostart Syntax void movetostart Move the current atom selection to the top lowest IDs of the atom list See the movetostart command for more details newatom Syntax atom newatom int string el double x 0 0 double y z 0 0 double vx 0 0 double vy 0 0 double vz fx 0 0 double fy 0 0 double fz 0 0 double 0 0 0 double Create a new atom in the model See the newatom command for more details newatomfrac Syntax atom newatomfrac int string
10. printvdw 163 337 printzmatrix 208 quit 248 random 198 randomi 198 readchars 222 readdouble 222 readdoublearray 222 readint 223 readintarray 223 readline 224 readlinef 224 readnext 224 readvar 225 readvarf 225 rebond 139 rebondpatterns 139 rebondselection 140 recreateexpression 176 redo 160 removecell 151 removelabel 196 removepoint 156 removereadoption 226 removestr 244 reorder 145 reorient 254 replacechars 243 replacestr 244 replicate 150 resetview 259 return 168 rewind 226 rotateview 259 rotx 145 roty 145 rotz 146 rules 177 runscript 229 savebitmap 194 saveexpression 177 savemodel 214 savemovie 194 scale 151 scalemolecules 151 scalename 156 scalevisible 156 sdminimise 206 searchcommands 248 seed 248 seekframe 251 select 232 selectall 233 338 selectf 233 selectfftype 233 selectfor 233 selectinsidecell 233 selectionaddhydrogen 146 selectioncog 234 selectioncom 234 selectline 234 selectmiller 235 selectmolecule 235 selectnone 235 selectoutsidecell 236 selectoverlaps 236 selectpattern 236 selectradial 237 selecttree 237 selecttype 237 setangle 255 setcell 152 setcharge 133 setcombinationrule 177 setcoords 133 setdistance 255 setelement 133 setforces 133 setfx 134 setfy 134 setfz 134 setid 134 setname 214 setpoint 157 setpointcolour 157 setpointvalue 157 setrx 134 setry 135
11. 11 3 Reading and Writing Formatted output in Aten is based largely on string formatting in C so if you re familiar with C then this should be a breeze If you re a Soldier of Fortran then the principles are very similar If you re familiar with neither then now s the time to learn 11 3 1 Formatted Output Formatted output corresponds to output to either the screen or to files and is used in the following commands Table 11 4 Formatted Output Commands Command Function error Write a message to the screen and immediately terminate execution of the current script filter command structure printf Write a message to the screen verbose Write a message to the screen provided verbose output mode is on writelinef Write a formatted line to the current output file writevarf Write a formatted string to a variable equivalent to the C sprintf command Basic Strings Formatting a string for output as mentioned elsewhere on numerous occasions works the same as for C The C printf command equivalent to the command of the same name in Aten takes a character string as its first argument and at its simplest this is all that is required caer MIL This prints Hello to the screen minus the quotes Importantly however a newline character is not printed meaning that the next thing you try and printf will appear on the same line For instance orcas Mas lO printf There would output HelloThere The
12. Aten v1 7 User Manual Last Updated Thursday 21 July 2011 TODO In command reference return types which are variable names and in Command Type style should be linked to relevant VType references Remove references to old region information in disordered builder New GUI images New description for Select window Topic Colourscales Topic Glyphs Topic Grids External Programs Section Examples Tutorials Section Disclaimer Aten comes with ABSOLUTELY NO WARRANTY This is free software and you are welcome to redistribute it under certain conditions For more details read the GPL at http www gnu org copyleft gpl html Aten is under continual development and tweaking If you have a feature suggestion a feature request or have found a bug or an idiosyncrasy please contact me at tris projectaten net Aten uses Space Group Info 1994 96 Ralf W Grosse Kunstleve the Qt toolkit Nokia and the readline library Some general notes First off if you find that Aten doesn t support the format you want consider writing a filter to do so And if you need help please ask More so if you find that Aten does support the format you want but doesn t appear to write it out correctly please let me know For forcefield expression files written with Aten I recommend that you check that the correct atom types get assigned to your molecule s Blind trust that this has actually occurred should only be employe
13. For example savebitmap bmp test bmp saves the current view to a file test bmp savebienapl pn or Opa o OOO SOOO ONE saves an enormous highly uncompressed png savemovie 194 Syntax void savemovie string filename string format int width 1 int height 1 int quality 1 int firstframe 1 int lastframe lt last gt int interval 1 Saves a movie of the trajectory associated to the current model Note that a valid movie encoder must be installed such as mencoder and arguments must be set in the program preferences see the Prefs variable Aten will first save a series of png images of the width height and quality specified to the temporary directory also specified in the preferences before passing them all to the provided encoder command The encoder arguments should contain both the text FILES and OUTPUT when it comes to running the commane Aten will substitute FILES for a wildcard list of image files and OUTPUT for the target movie filename Note that the format of the output movie is entirely guided by the options passed to the encoder command As with the savebitmap command if width and height are not specified the current dimensions of the view are used 800x600 if no GUI is present and the quality option determines the compression used on saved images The other arguments are self explanatory firstframe and lastframe give the range of trajectory frames which will be sa
14. Function members act in the same as subvariable members except that they take one or more arguments enclosed in parentheses immediately following the member name just as command functions do 8 2 2 Aten Type The master class type aten is there to provide access to various other structures such as the list of loaded models preferences element data etc It is available at all times from any command script or filter and is always called aten Note that it is not possible to declare new variables of type aten Table 8 2 Aten Type Members Member Type RW Description elements element Array of element data masses symbols names etc frame model The current model being displayed and the focus of editing i e the current trajectory frame or if no trajectory is 100 associated to the current model then the current selected model is returned model model The current model selected this is the parent model of a trajectory if a frame is currently being displayed models model Array of all loaded models currently available nelements int Number of chemical elements defined in the elements array nmodels int Number of models parent models i e not including trajectory frames currently loaded prefs prefs Program preferences 8 2 3 Atom Type Member Functions convertenergy Syntax double convertenergy double value string oldunits Convert the supplied energy value from oldunits to the current interna
15. Internal Colours Nu Primary ae Es gt 3 Figure 7 25 Grids Window Style page The general appearance of the selected grid can be modified in the Style page with the main rendering style set with the combo box see Section 16 10 for a list of possible styles Optionally a bounding box around the grid data may be drawn by selecting the Outline Volume checkbox The Periodic checkbox influences the way 3D surfaces are drawn close to the boundaries of the grid If unchecked a gap will appear near to the edges of the grid 81 volume since there is insufficient data with which to generate gradient information If checked data points on the opposite site of the grid will be used in this region useful for instance in the case of orbital information calculated in periodic systems Colours for the primary and if active secondary sufaces can be set to simple single colours by selecting Internal Colours and choosing whatever colour is desired from the colour selection buttons Should a more useful colouring scheme be desired than the surfaces may be rendered using a colour scale see Section 10 1 in which case the isovalue if volumetric or height if a 2D grid determines the colour of the data point To do so select From Colourscale and choose the ID of the colour scale to use from the ten definable in the program Grids o x File Edit Data Cutoff Origin Axes Style Shift lt gt xo gt o gt aj
16. angles bondconstraint HW Ow HW 4184 0 1 62398 end After giving the forcefield a name and defining the energy units used for the parameters the two types of atom described by the forcefield OW and HW are listed A unique id type name base element and type description are provided providing Aten with all it needs to be able to recognise and type these atoms within a model For each of these types the van der Waals data are provided in the Lennard Jones style inter 14 again the type id and type name are specified followed by the atomic charge and the epsilon and sigma values Note here that there are default combination rules set for each functional form see VDW functional forms for a list Finally the single bond and angle within the molecule are defined The type names involved in the interactions are given followed by the necessary parameters for the functional form specified constraint for the bond and bondconstraint for the angle And that s it Detailed explanations of each section follow A more complete test forcefield supplied with Aten can be found in data ff test ff 12 2 Supplied Forcefields A handful of forcefields ready formatted for import into Aten are provided with the code and are listed here It should be a relatively straightforward process to convert others unless the functional forms used are not yet implemented but sure if you ask then I will add them If you export an expression from Ate
17. previous item in the list since all such objects in Aten e g atoms are stored in lists containing many objects of the same type This makes iterating over say all atoms in a given model pretty easy for atom a aten model atoms a ta printf Atom id i is element s n a id a symbol In this example the variable a is declared and initialised to be a reference to the first atom in the current model The condition part simply consists of the expression a which effectively tests the reference address currently stored in a Since any positive number equates to TRUE see below for the if test the loop will continue until a contains no reference Since most all reference objects in Aten are stored internally in linked lists the prefix increment operator changes the value of the variable to be the reference of the next item in the list or 0 if there are no more items In this way the whole list of atoms can be traversed and neatly ended once the final item in the list has passed A variant of the for loop described above is the for in loop here only a control variable and initial value are supplied both of which must be of pointer types The loop itself will increase the value of the variable i e skip to the next item in the linked list until a NULL pointer is found For example select H for atom i aten model selection i i oenen Acon Saal tS SEleCtrechN aN LanG A for
18. 5 Model Selection Cell Definition Select or define a suitable model cell target Define a unit cell for the new model Relative Lengths Angles a 1 0000 90 00000000 0 b 1 0000 B 90 00000000 0 c 10000 Y 90 00000000 0 Final cell angles will be those set here while the final cell lengths will follow the ratios you set here with their absolute length determined by the cell contents lt Back Next gt Cancel As mentioned here we define exacly the angles of the cell but any lengths we specify are relative lengths which will be scaled according to the number and density of the molecules we choose to put in the cell We will leave them as they are for now so we will end up with a cubic cell with some side length 19 Zo Disorder Wizard oo Step 3 5 Choose Cell Partitioning Select a partitioning scheme to apply to the cell None No partitioning Number of partitions 1 The Disorder Builder normally permits a partitioning scheme see Section XXX to be selected in order to partition molecules up into different regions in the cell When generating a cell however this is not possible so we must choose the basic cell option and click Next Ae Disorder Wizard Voy Step 4 5 Choice of Components Select the models representing the components to be added to the cell Select models to use as components Next we must choose which models or components we wish to add into the new
19. A 169 9 11 Forcefield Commands Forcefield management and manual term creation angledef Syntax void angledef string form string type i string type j string type_k double datal Add an angle definition to the current forcefield form should correspond to one of the implemented angle functional forms while the three types refer to either type or equivalent names of defined atom types Up to ten data parameters may be supplied autoconversionunit Syntax Nw void autoconversionunit string unit Sets the target energy unit for automatic conversion of energetic forcefield parameters when writing out expresisons Can only be used within a file filter definition The unit parameter should correspond to one of the energy units recognised by Aten see energy units or may be omitted to specify that no conversion of parameters from the current internal unit of energy should take place Note that the conversion of energetic forcefield term parameters is performed only when accessing data through either the data member or parameter function of the forcefield atom forcefield bound or bound variable types For example autoconversiontype kcal indicates that no matter what the current internal unit of energy is all energetic forcefield parameters when accessed by the means listed above will be automatically converted into units of kcal bonddef Syntax void bonddef string form
20. Quantum Espresso SIESTA Flexible Data Format Tripos Sybyl Mol2 XMol XYZ Extension s akf datl fdat cif CONFIG REVCON ato log inp gjf gro arc mop mol msi pdb in fdf mol2 XYZ Table 1 1 Supported Model Formats Nickname ID R W Notes akf csd GRE dlpoly ato gamuslog gamusinp gjf gro arc mop mol msi pdb in siesta mol2 XYZ 1 7 8 2 18 11 17 14 16 10 12 13 15 9 6 RW RO RO RW RW RO RW WO RW RO RW RO RO RO Plain text format used by Aten Cartesian coordinates and Z Matrices Cartesian coordinates and Z Matrices Including periodic systems Cartesian coordinates only Assumes ibrav 0 Table 1 2 Supported Trajectory Formats Format Extension s Nickname Notes a wed HIS ISE dlpol ee HISTORY Pere Trajectories GAMESS US Trj File tr trj S PDB Trajectory ds Multiple PDB file pale pdb XYZ Trajectory Ery hts Multiple XYZ file eS 7 Table 1 3 Supported Grid Data Formats Format Extension s Nickname ID Notes Gaussian Cube cube cube 1 Also an importmodel filter Probability density pdens pdens 2 Simple 3D volumetric data format Surface surf surf 3 Simple 2D surface data format Table 1 4 Supported Expression Data Formats Format Extension s Nickname ID Read Write Notes FIELD DL_POLY FIELD file FIELD dlpoly 1 no yes Gromacs RTP file rtp
21. This is useful when one wishes to select a headgroup fragment attached to an atom without selecting the rest of the molecule The number of atoms selected by the process is returned For example int nclose selecttree 99 selects all atoms reachable by following chemical bonds from and including atom 99 selecttype Syntax int selecttype int string element string neta 237 Selects all atoms of the given element that also match the NETA description see Section 12 5 given allowing selections to be made based on the connectivity and local environment of atoms The number of previously unselected atoms matched is returned For example war MEZ selec MEM W ANA selects all carbon atoms that are bound to two hydrogens 238 9 27 Site Commands Describe sites within molecules for use in analysis Note These commands are outdated and may be removed completely in a future version getsite Syntax void getsite string name Selects makes current the site referenced by name If the site cannot be found an error is returned For example getsite carb1 makes the carb1 the current site listsites Syntax void listsites Prints the list of sites defined for the current model For example listsites newsite Syntax void newsite string name string atomlist Creates a new site name for the current model based on the molecule of pat
22. Unnamed001 lt lt no filename gt gt Modified Y YY File Edit View Selection Model Trajectory Forcefield Settings Scripts Help Je ABAXA Der DA t oesaeaRarseG Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle 1536 Atoms 9223 680000 g mol click drag or rotate in local frame right click drag ctrl remove from selection Orthorhombic 0 930293 g cm newmodel ice CEH A 501 To VES De SAO NO 90 S10 e newatomfrac 0 0 0 6648 0 0631 newatontrac OOo On Seon 00615 newatomfrac H 0 0 6636 0 1963 7 newatomfrac H 0 0 5363 0 0183 newatomfrac H 0 6766 0 2252 0 0183 spacegroup Cmc21 pack replicate 0 0 0 4 4 4 5 rebond 35 5 5 Exporting Coordinates in Bohr Filters Aten works in units of Angstroms but of course this does not suit every other computational code out there Many physics code allow or require input in units of Bohr The simplest way of generating coordinates in Bohr rather than Angstroms is to write a custom filter to output the data in the units that you want converting to from Angstroms on the fly This examples takes the existing xyz filter and creates a new xyzbohr filter that does reads and writes in Bohr note that Aten still works in Angstroms however Firstly copy the xyz filter that comes with Aten probably in usr share aten dat
23. and 0 5 0 0 0 5 representing the basic positions of atoms in a face centred cubic lattice Define Open the Cell Define Window Add a unit cell to the model by checking the Has Cell checkbox then go to the Define View ABC page and set the cell lengths a b and c to 1 0 then click Define Y Build Add the following four atoms to the model at the coordinates specified Change the current element to Na with Pick on the Edit page in the Build Window and use the Add Atom panel in the Tools page to create the atoms x 0 0 y 0 0 z 0 0 ee a eee Uy Oo ci a 05 A Aten vL7 11671 Unnamed001 lt lt no filename gt gt Modified Y YY File Edit View Selection Model Trajectory Forcefield Settings Scripts Help JA oI0Y DMA 0802 4 amp Transmute Click atoms to transmute into current drawing element shiftto transmute all atoms of the same element as the 4 Atoms 91 960000 g mol clicked atom Cubic 152 703154 g cm Create Interpenetrating Secondary Lattice 27 We need a second FCC lattice on which the chlorine atoms will sit We could add them all by hand but there are easier ways Ctrl A Select all the atoms in the model with the Ctrl A shortcut or go to the Edit Define menu and choose Select All Ctrl C Copy the current atom selection with Ctrl C or Edit Copy Ctrl V Paste the copied atoms with Ctrl V or Edit Paste Position Open the Position Window and select the Flip
24. command Multiple file extensions may be given separated by commas or whitespace File extension matching is case insensitive For example extension xyz means that files with extension xyz will be recognised by this filter extension xyz abc foo gt means that files with extensions xyz abc and foo will be recognised by this filter glob Syntax glob ext Sets the file dialog filter extension to use in the GUL and should be provided as a shell style glob For example glob doc filters any file matching doc in the relevant GUI file selector dialogs id Syntax id n When separate import and export filters for a given file type have been provided it is prudent to associate the pair together so that Aten knows how to save the data that has just been loaded in Each filter has a user definable integer ID associated with it that can be used to link import and export filters together For example if a model import filter has an ID of 7 and a model export filter also has this ID then it will be assumed that the two are linked and that a model saved with export filter 7 can be subsequently loaded with import filter 7 If the ID for a filter is not set it defaults to 1 and it is assumed that no partner exists and the file cannot be directly saved back into this format 270 For example id 13 See the list of supported formats in Table 1 1 to Table 1 4
25. double theta double ox double oy double oz Rotate the current selection by an angle theta in degrees about an axis defined either by the vector between two atom IDs or the vector components provided If supplied the rotation is performed using the coordinate origin specified by ox oy and oz otherwise 0 0 0 is assumed For example axisrotate 4 5 90 0 rotates the current selection 90 degrees about the axis formed by the vector between atom ids 4 and 5 4 gt 5 axisrotate 0 1 0 52 0 251 rotates the current selection 52 degrees about the y axis ax rsroraceilor i O S250 42 0 4250 AO rotates the current selection 52 degrees about the y axis but with the rotation centre at 4 0 4 0 4 0 centre Syntax void centre double x double y double z bool lockx FALSE bool locky FALSE bool lockz FALSE Centre the current atom selection at the specified coordinates The three optional arguments lockx locky and lockz specify one or more atomic coordinates that are to remain unchanged during the transformation For example comu 0 0 00 15 0 i centres the current selection at the coordinates 0 0 15 flipx Syntax void flipx Flip negate the x coordinates of the current selection For example flipx flipy Syntax void flipy Flip negate the y coordinates of the current selection For example 252 flipy flipz
26. double vdwenergy 122 Calculates and returns the total van der Waals energy for the current model 8 2 33 Pattern Type The pattern type describes a single continuous collection of similar molecules fragments within a model Table 8 21 Pattern Type Members Member Type RW Description angles bound Array of angle interactions in one molecule of the pattern atoms atom Array of atoms spanned by the pattern bonds bound Array of bond interactions in one molecule of the pattern ff forcefield Reference to the forcefield associated to the pattern if any ffangles ffbound List of unique forcefield angle terms in the pattern ffbonds ffbound List of unique forcefield bond terms in the pattern fftorsions ffbound List of unique forcefield torsion terms in the pattern fftypes ffatom Array of unique atom types used in the pattern firstatom atom Reference to the first atom spanned by the pattern firstatomid int Atom ID of the first atom spanned by the pattern fixed int Whether the coordinates of all atoms in the pattern are fixed in minimisation routines lastatom atom Reference to the last atom spanned by the pattern lastatomid int Atom ID of the last atom spanned by the pattern name string e Name of the pattern nangles int Number of angles in one molecule of the pattern natoms int Total number of atoms spanned by the pattern nbonds int Number of bonds in one mo
27. gridcoloursecondary Syntax void gridcoloursecondary double r double g double b double a 1 0 Set the internal colour of secondary grid surface to the RGB A value supplied each component of which should be in the range 0 0 to 1 0 inclusive For example gridcoloursecondary 0 9 0 9 0 9 sets the secondary surface colour to off white gridcolourscale Syntax void gridcolourscale int id Set the colourscale to use for the current grid to the colourscale ID specified which should be in the range 1 10 If 0 is given as the argument the internal colour of the grid data is used Linking a colourscale to a grid will result in the minimum and maximum ranges of the grid being recalculated to ensure all points in the grid are covered by the scale whose range is adjusted if necessary For example gridcolourscale 4 colours the grid data according to colourscale 4 gridcolourscale 0 uses the internal colour s specified for the grid gridcubic Syntax 189 void gridcubic double 1 Sets up a cubic system of axes for the current grid For example Gcaoleuloa c 0 5 p sets up a cubic system of axes each grid point 0 5 A apart in all directions gridcutoff Syntax void gridcutoff double lowercut double uppercut Sets the lower and 1f supplied upper cutoff values for the current grid For example arteria OP OO ADO sets the lower grid cutoff for the
28. gt aten original xyz c selectall copy paste 10 10 10 savemodel xyz pasted xyz quit Multiple sets of commands may be given bob pec gt aten source xyz c selectall copy target xyz c paste 10 10 10 Take care here since the commands provided act on the current model i e the one that was most recently loaded Commands are available that select between the loaded models see the list of model related commands in Section 9 22 cachelimit lt limit gt 46 Sets the size limit for trajectory loading in kilobytes If an entire trajectory will fit into this cache all frames in the trajectory are loaded immediately If not frames will be read from disk as and when required centre Force translation of non periodic models centre of geometry to the origin even if the centre command was not used in the corresponding filter D d lt type gt debug type Enables debugging of subroutine calls so that program execution can be traced or enables extra debug output from specific types of routines if type is given Warning this creates a lot of output most of which is incomprehensible to people with their sanity still intact but is useful to track the program up to the point of say a hideous crash Valid type values are listed in Output Types in Section 16 13 double lt name value gt Creates a floating variable name which is of type double and that can be accessed from a
29. int getline string destvar Read an entire line from the input file and put it in the character variable provided The line also becomes the current target for readnext The command returns a Read Successinteger 220 For example string nextline int n getline nextline gets the next line from the file and places it in the variable next line nextarg Syntax int nextarg int i int nextarg double d int nextarg string s Read the next whitespace delimited chunk of text from the current file and place it in the variable supplied Note that this command reads directly from the file and not the last line read with getline or readline see the readnext command to read the next delimited argument from the last read line The command returns TRUE 1 if an argument was successfully read or FALSE 0 otherwise e g if the end of the file was found The command will accept a variable of any ordinary type int double or string as its argument Conversion between the text in the file and the target variable type is performed automatically For example int i int success nextarg i peekchar Syntax string peekchar Peeks the next character that will be read from the source file and returns it as a string The actual file position for reading is unaffected For example string char peekchar peekchari Syntax int peekchari 221 Peeks the next character that w
30. see Bond Types in Section 16 2 required for a bound atom The keyword should be used inside bracketed parts of bound atom descriptions It is important to note that the bond keyword should only be used in conjunction with the x any bond to specifier since the specific connection demanded by the X and X specifiers will override any bond declarations Table 12 5 NETA bond Keyword Examples Command Meaning O bond double A double bond to an oxygen atom equivalent to 0 amp 55 bond triple A triple bond to an atom which matches type ID 55 see Reusing Types in section 12 5 4 C bond single A single bond to a carbon atom a very explicit way of writing simply C chain The chain command provides an easy was of specifying a linear sequence of atoms from the current atom forward Within the bracketed part a sequence of connections are listed in the order in which they are to appear Atoms in the chain are specified in the same way as other connections e g C nbonds 2 but should not be separated by commas The repeat keyword n may also be specified at some point in the bracketed part to define that more than one of the defined chains is required Note that if all atoms specified for the chain are matched but the actual chain in the model is longer a positive match will be returned Thus 1t is usually a good idea to define the last atom in the chain more explicitly to prevent false matches Table 12 6 NETA chain
31. setrz 135 setvelocities 135 setview 259 setvx 135 setvy 135 setvz 135 shiftdown 146 shiftup 146 show 136 showall 214 sin 198 siteaxes 240 skipchars 226 skipline 226 spacegroup 152 speedtest 260 sprintf 244 339 sqrt 199 stripchars 245 tan 199 toa 245 torsiondef 177 translate 256 translateatom 256 translatecell 256 translateview 260 translateworld 257 transmute 147 typedef 178 typemodel 178 typetest 178 undo 160 units 179 uppercase 245 veut 164 vdw 179 verbose 203 viewalong 260 viewalongcell 260 while 169 writeline 227 writelinef 227 writevar 228 writevarf 228 zoomview 261 forcefield keywords angles 294 bonds 295 convert 294 data 295 defines 296 equivalents 297 function 297 generator 298 inter 298 name 293 torsions 299 types 299 uatypes 300 units 293 NETA keywords any bond to 310 aromatic 313 bond 311 chain 311 double bond to 311 linear 314 n 312 nbonds 312 340 nh 312 noring 313 octahedral 315 onebond 314 planar 313 ring 313 single bond to 310 size 314 sqplanar 315 tbp 315 tetrahedral 315 trigonal 315 tshape 314 unbound 314 Patterns 15 264 Default 264 types aten 100 atom 101 basisprimitive 102 basisshell 103 bond 103 bound 104 colourscale 104 colourscalepoint 105 eigenvector 105 element 106 energystore 106 ffatom 106 ffbound 108 forcefield
32. supplied arguments The contents of the arguments are formatted according to their type and suitable internal defaults A newline character is appended automatically to the end of the written line For example writeline Number of atoms aten model natoms writes a line indicating the number of atoms in the model to the current output file writelinef Syntax void writelinef string format Write a formatted line to the current output file according to the supplied format and any supplied arguments Usage is the same as for the printf command Note that a newline character is not automatically appended to the end of the written line and one should be written explicitly using the escape sequence n For example Wencehiner ss S8r ni Number Of atoms aten model natos 227 writes a line indicating the number of atoms in the model to the current output file e g Number of atoms 3 writevar Syntax void writevar string dest Write to the supplied string variable dest the whitespace delimited contents of the supplied arguments The contents of the arguments are formatted according to their type and suitable internal defaults A newline character is appended automatically to the end of the written line For example string s writevar s Number of atoms aten model natoms writeline s same result as the example for the writeline command except that the final string
33. to a value of 3 3 and white colour setpointcolour Syntax void setpointcolour int scaleid int pointid double r double g double b double a 1 0 Sets the colour of an existing point in the specified colourscale For example Seirjooumecollowme S it O40 O20 1 0 sets the first point on colourscale 5 to be coloured blue setpointvalue Syntax void setpointvalue int scaleid int pointid double value Sets the value of an existing point in the specified colourscale For example setpointvalue 4 3 0 1 sets the third point of colourscale 4 to a value of 0 1 157 9 7 Disorder Commands Set up the disordered builder to create systems from individual components using Monte Carlo methods disorder Syntax void disorder string scheme XXX Start the disordered builder requesting ncycles cycles of Monte Carlo moves For example disorder 50 runs 50 cycles of the disordered builder listcomponents Syntax void listcomponents Prints a list of the currently requested populations for all models to be added during the disordered building process For example listcomponents 158 9 8 Edit Commands Standard editing commands copy Syntax void copy Copy the current atom selection to the clipboard ready for pasting For example copy cut Syntax void cut Cut the current atom selection to the clipboard Fo
34. torsiongenerator Syntax int torsiongenerator ffbound newdata atom i atom j atom k atom 1 Called whenever function data for an unrecognised torsion between the atom types currently assigned to atoms i j k and 1 is needed Generated parameters should be store in the passed newdata structure vdwgenerator Syntax int vdwgenerator ffatom data Called whenever descriptive VDW data is missing from an atom type which is passed into the function and should have the correct data placed in it 303 12 5 Typing We are all familiar with talking about atoms being chemically different depending on the functional group in which they exist e g ether carbonyl and alcoholic oxygens and this categorisation of atoms forms basis of forcefield writing That is a large number of different molecules and types of molecule should be described by a small set of different atoms 1 e atom types At the simplest level the connectivity of an atom is enough to uniquely identify its specific type Some methods to use this information to uniquely assign types to atomic centres involve deriving a unique integer from the local connectivity of the atom e g the SATIS method REF XXX but including information beyond second neighbours is rather impractical Others use a typing language to describe individual elements of the topology of atoms in molecules and are flexible enough to be able to describe complex situations in a more s
35. variable i e the variable that changes on each loop iteration and optionally its starting value the condition is tested on each loop iteration to see whether or not to continue with the loop and finally the increment is an expression to modify the control variable after each iteration setting it to a new value If multiple commands are to make up the body of the loop 165 executed on each iteration then they should be enclosed in curly brackets as written in the syntax above If only a single command is executed on each iteration the curly brackets may be omitted Some examples oa ligne Silo SiO al bd Orue aa ak 2 Loop over and print all integers between 1 and 10 A local variable i is declared and initialised all in one go in the startvalue part of the loop The long way of incrementing the integer variable i i 1 is typically not used in C C most people preferring to take advantage of the C s useful postfix and prefix operators as in the next example scone bey 1007 mOi 200 orim WC oibimicsbiare elote no CENAN LA Here an existing variable n is decreased from 100 to 1 printing out all numbers along the way Note the usage of the double minus operator the prefix decrease operator which decreases its associated variable in this case n For integers to decrease means to reduce the value by 1 For other types the meaning may vary for instance with reference types the operator means
36. 1 e the corresponding entry in the inter block will be 24 Cl O ORES S50 298 Some functional forms have default values for some parameters used in the functional form and need not be specified if there are any these are shown in Section 13 1 For this reason it is important not to add any unnecessary extra data to the entries in the inter block since this may overwrite a default parameter that results in literal chaos torsions Syntax torsions form escale vscale typename i typename j typename k typename_l datal data2 end Definitions of intramolecular torsion terms are given in torsions blocks Multiple torsions blocks may exist each defining a subset of terms and each possessing a different functional form specified by the form argument see Section 13 4 for a list of valid forms For torsions the electrostatic and VDW 1 4 interactions i e those between atoms i and 1 ina torsion i j k 1 are scaled by some factor between 0 0 and 1 0 The optional escale and vscale arguments specify these scaling factors if they are not provided they both default to 0 5 The four typenames identify the particular torsion to which the parameters are relevant Note that typenames given for a torsion i j k 1 will also match a torsion 1 k j i Data parameters should be provided in the required order for the specified form For example torsions cos ETICO CAE O 30 0 OR end provides parameters for an H C O H torsion
37. 108 glyph 111 glyphdata 112 341 grid 112 measurement 113 model 113 pattern 123 prefs 124 unitcell 128 vector 129
38. Build Window change the active element on the Edit page to aluminium by clicking the periodic table button Rm and selecting it there On the Add Atom panel in the Tools page make sure Fractional Coordinates is checked and then enter the following sets of coordinates clicking Add after each set is entered x 0 9166 y 0 0 z 0 2073 x 0 6595 y 0 0 z 0 3165 Go back to the the Edit page and change the active element to oxygen by clicking the amp button Then return to the Tools page and add three more atoms at the following fractional coordinates x 0 8272 y 0 0 z 0 4273 x 0 495 y 0 0 z 0 2526 x 0 1611 y 0 0 z 0 0984 A Aten vL7 11671 Unnamed001 lt lt no filename gt gt Modified y o e File Edit View Selection Model Trajectory Forcefield Settings Scripts Help JARA DY RBA EEO E Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click 5 Atoms 101 961000 g mol drag or rotate in local frame right click drag ctrl remove from selection Parallelepiped 0 900964 g cm Assign the Spacegroup and Pack To complete the model the spacegroup of the crystal must be set so that generation of the symmetry related atoms can be performed This is all done on the Cell Define window The spacegroup can be entered as either its numeric ID as listed in the IUC Tables or as the unformatted spacegroup
39. Cubic 1 000000 g cm Script When run from the command line the disorder builder always requires a model with a unit cell to be defined only through the GUI is the model created automatically This script defines a basic cubic cell in a new model before the disorder builder is run with the second argument set to FALSE which indicates that the cell size is not fixed and should be adjusted to suit the defined molecule contents and also minimises the system a little before saving out coordinates and a forcefield expression for DL_POLY newmodel water newatom 0 addhydrogen setupcomponent both 1 200 1 0 newmodel box call iL 0 iLO 10 90 20 90 9 disorder None FALSE load ENUS PES MEE mcminimise 20 sdminimise 20 saveexpression dlpoly water FIELD 21 savemodel dlpoly quit water CONFIG 22 5 2 Building 0 Alumina from Basic Crystal Data Crystal structures are useful for many things provided you can find them in electronic format When you can t and are left with the bare crystallographic data in a paper things are slightly more troublesome This was exactly my experience when working with 0 alumina the crystal information is readily available in a paper by Zhou and Snyder Acta Cryst B 47 617 1991 and here s how to make use of it Create the Unit Cell First we create the crystal cell in which to add our atoms From the paper we see it is a
40. DY g Disorder Wizard d O ow 1 Step 1 5 Model Target Step 2 5 Model Selection Cell Definition Select the target model for the build or choose to create anew one Select or define a suitable model cell target Use Existing Model Select an existing model to use as the target Select a loaded model which already has a cell definition as the target for the disordered builder The model may have existing contents which will be preserved during the build An optional partitioning scheme may be applied Create New Model and Define Cell A new model will be created and used as the target for the disordered builder The unit cell will be defined in the next step and an optional partitioning scheme may be applied O Create New Model and Generate Cell A new model will be created and used as the target for the disordered builder The shape ofthe cell will be defined in the next step while the final size will depend on the specified contents No partitioning scheme other than none may be selected in this mode lt Back Next gt Cancel lt Back Next gt Cancel We wish to add in water to an existing system in this example so choose the top option Use Existing Model and press Next You then need to choose the target model for the builder which is the extended NaCl system we just created Select it and press Next 30 g v Disorder Wizard Y Y DY Step 3 5 Choose Cell Partitioning Select a partitioning schem
41. Flag whether manual swapping of GL buffers is enabled Maximum allowable number of rings to detect within any single pattern Maximum size of ring to detect when atom typing Maximum number of undo levels remembered for each model 1 unlimited Update frequency for the current model in various methods Location of MOPAC executable including full path Current actions of the Left Middle Right and Wheel mouse buttons Sets the degree to which mouse move events are filtered with 1 being no filtering Use this to reduce update lag on sluggish systems Enables disables multisampling hardware aliasing Flag controlling whether OS stored Qt settings are loaded on startup Whether perspective view is enabled Field of vision angle to use for perspective rendering Enables disables polygon aliasing The current model drawing style The general rendering quality i e replicatefold replicatetrim reusequality selectionscale shininess specularcolour spotlight spotlightambient spotlightdiffuse spotlightposition spotlightspecular sticknormalwidth stickselectedwidth tempdir textcolour transparencybinwidth transparencycorrect transparencynbins transparencybinstartz unitcellaxescolour unitcellcolour useframebuffer int int int double int double 4 int double 4 double 4 double 4 double 4 double double string double 4 double int int double doub
42. Gola IE OI A A A ia 45 0 2 7 e o O A ees ad eee ee a aie 45 032 Batch Processing Modes a alada age tas 52 DS oo ied etc dia Se tea co a vaca cs Aa os tes ae ee 54 Pl HEMET LG os oe iene a tine Ms aie E tue Maite 54 AA A aad Seats Sietiescal eit acs ouletasttiaads a Dacstet 55 T3 SKEYDOATC S HOM CUES sig da is EI nr 57 T Th Main Toolbar sietst nl aster insna decido 58 Te Mhe Tool BOR arrinin i a E a A cere Soren S 60 LOS Atom List WAndOW sii too 61 Tele Bild WANG OW se carts 1c adele tlds cts ea rect Ss wa e as beac sa eeroct hs la tit SES 62 T8 Sell Detintion Window siese A ae ea eee 64 19 Cell Transforma W INOW satis 65 AIN RS A BCA A GOS CSE hE 67 TAL Disorder builder Wizard a ie edt ad 70 T42 Forcefields Window sc aoe ia oi a 73 7 143 Fragments Wind Winnie 76 1 14 Geometry Window isc aii rs 78 1 15 Glypls WihdO Wii dci 79 T16 Grids Window ri hee A a ree 80 TAL Messages WIN Weiss di 83 7 18 POSITION Wind Weil co asec sd onde ee A ca dec ics obi oe Deke da Nelo id tad 84 TIO Select WindOW aiii ta 87 7 20 Trajectory Window airis svssad ss danscncandesansvanssaatassasea a a ias 89 Pie bes e WNdOWs aa nuadss lobbed ages tain atten doe ual latinas aaghenecenacss 90 N22 IIA Wind OW cco A os aS gt et e A A a das eae A 93 Command AN SUA Se eee cides laste let A A A 94 SL Command Panga ce Oy erview a os 94 8 2 1 Vatlableniypesiscce entitle ie Gian adda tote aan edie eee ns ais 100 Command RELEASE A eee
43. Provides interactive shell Load amp run scripts ZA Z Mattix Edit Z matrix for the current model Y Build Draw atoms chains of atoms and bonds Rebond amp clear bonds Transform Transform the current atom selection e g flip rotate matrix multiply XS Fragments Access to molecular fragments when in fragment drawing mode Position Position the current atom selection e g shift translate centre Define Define create cell for the current model g Transform Transform the cell for the current model amp Disorder Run the Disorder builder 7 Geometry Measure distances and angles Edit geometry of current atom selection Y FF Energy Load edit forcefields Perform geometry optimisation of models S Selection Advanced atom selection tools Y cis Grid manipulation and editing Ps Glyphs Glyph manipulation and editing a Vibrations Visualisation of molecular vibrations if present CE Trajectory Visualisation of associated trajectory if present 60 7 6 Atom List Window The Atom List window provides a list of all atoms in the current model or frame displaying elements charges and positions If patterns have been defined for the model see Section 10 3 the atoms in the list will be grouped according to their encompassing pattern otherwise they are listed in one continuous run by ascending ID Atom List o x Patten ID E X Z View By e Atom Pattern Na Na Actions Yv FTX Figure 7 3 A
44. Qt4 dock areas in which the toolbox and any of the tool windows can be placed Once you have the various subwindows set up how you like them press Settings Store Default Window State to remember these settings for when Aten next starts 54 7 2 Mouse Control Each of the mouse buttons has a different style of action on the canvas each of which can be set to the user s taste in the preferences menu item Settings Preferences on Linux Windows In addition the Shift Ctrl and Alt keys modify or augment these default actions performed by the mouse Standard settings out of the box are Table 7 1 Mouse Button Actions Button Key Modifier Action Click on individual atoms to select exclusively Let Dong Click hold drag to exclusively select all atoms within rectangular region Click on individual atoms to toggle selection state Shift A PE Click hold drag to inclusively select all atoms within rectangular region Click on individual atoms to toggle selection state Ctrl y eo Click hold drag to inclusively deselect all atoms within rectangular region Click hold drag to rotate camera around model Right None Click on atom to show context Selection menu Shift Click hold drag to rotate view around z axis perpendicular to plane of screen Ctrl Click hold drag to rotate selection in local model space Click hold drag to rotate selection around z axis in local Ctrl Shift model space Middle None Click hold drag to trans
45. Select the first frame from trajectory of current model For example firstframe 249 lastframe Syntax void lastframe Select last frame in trajectory of current model For example lastframe loadtrajectory Syntax int loadtrajectory string filename Associate trajectory in filename with the current model An integer value of 1 is returned if the association was successful or 0 otherwise For example int success loadtrajectory home foo md water HISf opens and associated the formatted DL_POLY trajectory file water HISf with the current model nextframe Syntax void nextframe Select next frame from trajectory of current model For example nextframe prevframe Syntax void prevframe Select the previous frame from the trajectory of the current model For example 250 prevframe seekframe Syntax void seekframe int frameno Seeks to the frame number specified For example seekframe 10 seeks to the 10th frame of the current trajectory 9 31 Transform Commands Commands to transform the current selection of the model axisrotate Syntax void axisrotate atom int i atom int i double theta void axisrotate atom int i atom int i double theta double ox double oy double oz void axisrotate double x double y double z double theta void axisrotate double x double y double z
46. Table 16 3 Bound type keywords Value Description angle A normal angle interaction between three bound atoms bond A normal bond interaction between two bound atoms improper An improper torsion between four not necessarily bound atoms torsion A proper torsion interaction between four bound atoms 326 ub A Urey Bradley 1 3 term between two atoms at the extreme of a related angle 16 4 Cell Types A model s unit cell is at any given time one of the following Table 16 4 Cell type keywords Value Description none The model has no unit cell i e it is non periodic cubic The model s unit cell is cubic with A B C and alpha beta gamma 90 orthorhombic The model s unit cell is an orthorhombus with any cell lengths and alpha beta gamma 90 parallelepiped The model s unit cell is monoclinic or triclinic with any cell lengths and angles 16 5 Colour Schemes Available atomic colouring schemes are Table 16 5 Colour scheme keywords Value Description charge Atoms and connected bonds are coloured according to their charge element Atoms and connected bonds are coloured according to their element force Atoms and connected bonds are coloured according to the force acting on the atom velocity Atoms and connected bonds are coloured according to the velocities of the atoms custom Atoms and connected bonds are coloured according to the custom colours set on individual atoms 16 6 Combination Rules Combination rule equatio
47. a term is found that is not satisfied however the score is reset to 1 and the match will fail All terms in a type description must be satisfied in order for the type to be assigned to an atom Empty Types Score 1 A type description containing no terms has a maximum score of 1 coming from a match of the element type Hence 99 Cgen C a Generic carbon matches any carbon in any system but will be replaced fairly easily by other types since it has such a low score Normal Types Score gt 1 For a type in which all terms are matched successfully one point is scored for each individual term All of the following types have a potential maximum score of 3 don t forget one point comes from matching the element 100 Gale a nbonds 2 linear Carbon A 101 52 E WAC CN Carbon B 102 Cs iS Ca T 20 ay Carbon E 102 C4 C Carbon D Moreover they all potentially match the same atom for example the central carbon in 1 2 propadiene Since they have the same score the first type C1 will match and persist over the other three since only types with higher not equivalent scores can replace it 12 5 4 Reusing Types Once a complex NETA definition has been made for a given atom type it is often useful to be able to reference this type in order to save repeating the same description for a closely bound atom The ampersand symbol allows you to do this and specifies an integer type id to match rather than an eleme
48. a value of 1 if the data was read successfully and should return 0 if an error is encountered Header Data When opening a trajectory file with an importtrajectory filter the first thing Aten does is attempt to read any header information from the file by calling the readheader function defined in the filter Since a trajectory file may not contain a header and consists simply of individual frames back to back in these situations the readheader function defined in the filter should not read any data The filter definition then becomes simply filter type importtrajectory name Example Filter Template int readheader No header so just return return 1 int readframe Code to read frame data goes here Here the readheader function always succeeds so Aten always thinks it has successfully read a header Frame Data If readheader is successful Aten proceeds to read the first frame by calling the readframe function in order to get an idea of the size of an individual frame and hence the total number of frames in the trajectory Of course this assumes that all frames take up the same number of bytes in the file and may not always be the case especially for plain text 280 trajectory files Thus the frame estimate output by Aten should not necessarily be taken as gospel Unless an error is encountered when reading the test frame i e readframe returns 0 or FALSE the tr
49. additional argument For example primer Msn an es Festa Wal ILO 9 will print This number is 10 Similarly int value 1234 Prints Ecos tant a tales NO ae 284 will print Constant risa area Meis male san There are other specifiers suitable for different types of data see Section 11 3 4 The way data is presented by the specifier in the final output can also be controlled e g for numerical arguments the number of decimal places presence of exponentiation etc can be defined 11 3 3 Formatted Input Formatted input corresponds to input from either files or string variables and is used in the following commands Table 11 5 Formatted input commands Command Function readlinef Read a formatted line from the current input file readvarf Read a formatted string from a variable Note that the meaning of the formatting string changes slightly here in essence the type and formats of the specifiers are used to break up the supplied string into separate arguments which are then placed in the provided corresponding variable arguments When reading in string data note that blank characters are significant and will be retained To strip trailing blank characters spaces and tabs when reading a fixed length string in a format supply the length as a negative number 11 3 4 Specifiers The list of allowable variable specified corresponds more or less exactly to that found in C with some small omissions and minor in
50. all atoms that are within a distance radius from a line whose direction is 1x ly 1z and which passes through the point x y z The number of newly selected atoms is returned For example selec OOO OO ON selects all atoms within 5 of a line running through the origin along the Cartesian z direction selectmiller Syntax int selectmiller int h int k int 1 int inside FALSE Select all atoms that are outside the specified Miller plane and its mirror if it has one If the final parameter is specified as TRUE then atoms inside the specified Miller plane and its mirror are selected For example selec Lei als A selects all atoms located beyond the 111 plane in the unit cell selectmolecule Syntax int selectmolecule atom int target Select all atoms in the molecule fragment to which the supplied target atom belongs For example selectmolecule 5 selects the bound fragment in which atom number 5 exists selectnone Syntax void selectnone 235 Deselect all atoms in the current model For example selectnone selectoverlaps Syntax int selectoverlaps double dist 0 2 Select all atoms that are within a certain distance of another or the default of 0 2 A if no argument is provided The number of selected overlapping atoms is returned For example int noverlaps selectoverlaps 0 1 selects all atoms that are less
51. are specified in the form of blocks Each keyword in this section marks the start of block and must at some point be terminated by an end keyword Blocks contain one or more lines of data the contents of which is detailed in each section In addition each keyword may take one or more optional or required values angles Syntax angles form typename i typename j typename k datal data2 end Definitions of intramolecular angle terms are given in angles blocks Multiple angles blocks may exist each defining a subset of terms and each possessing a different functional form specified by the form argument see Section 13 3 for a list of valid forms The three typenames identify the particular angle to which the parameters are relevant Note that typenames given for an angle i j k will also match an angle k j i Data parameters should be provided in the required order for the specified form 294 For example angles harmonic BHE CID hee 80 0 109 4 end provides parameters for an H C H angle using the harmonic potential bonds Syntax bonds form typename i typename j datal data2 end Definitions of intramolecular bond terms are given in bonds blocks Multiple bonds blocks may exist each defining a subset of terms and each possessing a different functional form specified by the form argument see Section 13 2 for a list of valid forms The two typenames identify the particular bond to which the paramete
52. assigns a charge of 0 1 to the third atom in each molecule of the current pattern chargetype Syntax void chargetype string fftype double q Assigns a charge of gto each atom that is of type fftype in the current model For example chargetype OW 0 8 gives a charge of 0 8 to every atom that has an assigned typename of OW clearcharges Syntax void clearcharges Clears all charges in the current model setting them to zero For example clearcharges 154 9 6 ColourScales Commands Define colourscales to colour objects Each colourscale has a number of points defining colours at specific values between adjacent points the colour is linearly interpolated Points in acolourscale are numbered from 1 onwards There are ten available colourscales with IDs 1 10 Some of these have specific uses within Aten Colourscales for a discussion of colourscales and how they may be used within Aten addpoint Syntax void addpoint int scaleid double value double r double g double b double a 1 0 Adds a new point to the end of the specified colourscale at the point value and with the RGB A colour provided each component of which should be in the range 0 0 to 1 0 inclusive For example aelooimo l 15 0 050 LO 00 adds a point to colourscale 1 at a value of 15 0 in a nasty green colour clearpoints Syntax void clearpoints int scaleid Clears all points from th
53. atom i and the reference atom j Note that the coordinates of both i and j are not modified in any way translateatom Syntax vector translateatom atom i double dx double dy double dz Returns a vector corresponding to the original coordinates of atom i translated by the specified fractional cell amounts in each cell axis direction Note that the existing coordinates of i are not modified in any way 8 2 39 Vector Type The vector type is a simple 3 vector class containing three double values 129 Table 8 24 Vector Type Members Member Type RW Description mag Xx y Z doubl doubl doubl doubl e e e e Magnitude of the vector Setting this value rescales the vector The x component of the vector The y component of the vector The z component of the vector 130 9 Command Reference 9 1 Atom Commands Define and set properties of atoms atomstyle Syntax void atomstyle string style Sets the individual drawing style for the current atom selection used when the global drawing style is individual For example atomstyle tube sets the current atom selection to be drawn in the tube style Drawing Styles for a list of available styles currentatom Syntax atom currentatom atom currentatom atom id id Return a reference to the current atom If a new atom id is provided the current atom is set before being returned For example atom i getatom
54. ats a ld Setters a tags 13 4 A A NN 15 Abe e ea a 15 o File OC AUOMS oeie e iior dicted nate orie esie Oat RacesGulatcat tes e tis 16 4 3 AA A A a haul taash e a a ETTET saves 17 De Usage Examples ssie een e ania a e E Ea E En ENTO E SENESE 18 5 1 Creating a Bulk Water Model GUD vision dae 18 5 2 Building 0 Alumina from Basic Crystal Data ooooonocnnconocinocconcnononancnnnonncnncconanncnnnonos 23 5 3 Creating an NaCl Water Two Phase System GUI ooooonnocccnnococonccccconccononanonancncnnnanos 27 5 4 Building Ice I from Crystal Information GUD cooccnnccninccnonononnnonancnoncnoncnanncnnncconncnn 33 5 5 Exporting Coordinates in Bohr Filters oooncccnnnicinoniccnoncccnnnnncnnncnononcnonnncncnnncncnnnnnos 36 5 6 Calculate Average Coordinates CLD Si A ak eee 38 5 7 Self Contained Liquid Chloroform Builder Script ooooonoccnnnccnnnonionononccannnonnonnncnnn 39 5 8 Generating Images Without the GUI CLD ooonoccnncccnocaninncoonoconnnonnnononcnnnnnnnncnnnccnn anno 40 i 5 9 Calculating a Torsion Energy Profile CLD oooonnncccnnnccononcccnoncncnnnnnnnoncnonnnnnonancnnnnnanos 41 5 10 Running a Script on Many Models CLI Batch ooonnncnnoncnonconocnnonccnoncnonnnonnncnnncnn 42 5 11 Saving GAMESS US Input with Options CLD oooooonnncccnnncccconcccnoncnonnnacononacinnnonos 43 5 12 Printing all Bond Distances in a Model CLD oooconoccnnocococonacninanonanononcnannnonncnonacnn 44 Command LUST e e boe 45
55. bob pe gt configure with qt fink with qtdir lt path gt where lt path gt points to the location of the Qt4 development binaries All being well no errors should be encountered by either of these two scripts Check out the FAQ for some commonly encountered problems If you get find yourself up against unresolvable issues please email me and Pll try to help CMake An out of tree build is best Make a directory somewhere enter in to it and run bob pc gt cmake path to source for aten nn mm For example bob pec gt cd bob pec gt mkdir aten build bob pc gt cd aten build bob pc gt cmake src aten 1 7 2 2 4 Compile Once successfully configured build the source with bob pc gt make This is probably a good time to make tea or brew coffee 2 3 From Source Windows Note that these instructions were written from the perspective of a Windows XP system It s likely that the procedure for Vista Windows 7 etc will be similar First step download and install the following 2 3 1 Install Visual Studio C 2010 Get the C version of Visual Studio from http www microsoft com express Windows at the time of writing this was version 10 0 but earlier versions 8 0 and 9 0 are also fine This will download a small web installer to your machine called vc_web exe Run this and accept the license You may choose not to install Silverlight since it is not necessary for Aten Remember where th
56. capabilities of the select and deselect commands from within the GUI The total number of atoms selected along with their empirical formula is also displayed Select o x Actions Se All None PY Invert ae Expand Selection by ID Element Select Deselect Select by Description NETA Element C Boa Select Deselect Current Selection Total selected 0 Figure 7 33 Select Window Basic atom selection operations can be made using the All None Invert and Expand buttons at the top of the window The first three are self explanatory selecting all atoms no atoms and reversing the current selection respectively The final button Expand looks at any bonds attached to any currently selected atoms and selects those atoms that are bound as well Only the immediate bound neighbours of each atom are considered each time the expansion is made Three more advanced selection methods are also available Selection by ID Element Ranges Ranges of atom IDs and or elements are specified as a b where a and b are either both atom IDs or both element symbols In addition the symbol can be used before as in a or after as in a an atom ID or element symbol to mean respectively everything up to and including a or a and everything after Multiple selection ranges may be given separated by commas Selection or deselection of atoms based on the defined range s is made by the Select and Deselect buttons
57. current forcefield to the current pattern or one specified by either a reference integer ID in the current model or a pattern pointer For example ffpattern associates the current forcefield to the current pattern ffpattern bulk associates the current forcefield to a pattern named bulk in the current model finaliseff Syntax void finaliseff 173 Perform necessary operations on the current forcefield once all data has been added Must be called fixtype Syntax void fixtype int typeid atom int id 0 Set the current atom selection or the specified atom to have the type id in the current forcefield specified Types set in this manner will not be overwritten by tha typing routines allowing specific types to be applied above the normal rules Note that the type s NETA description is not checked and so any even types not matching the base element may be applied in this way For example y peda OE WINDY MINDY IN VEC ina ES CMS CAOS SIS 9 assigns newly created type 99 specific to nitrogen to all carbons in the model fixtype Syntax void freetype atomlint id 0 For the current atom selection or the specified atom free any previously fixed types For example freetype 14 frees any previously set type on atom 14 getcombinationrule Syntax string getcombinationrule string form string parameter Returns the combination rule in use for t
58. current grid to 0 002 and the upper grid cutoff to 0 005 gridcutoffsecondary Syntax void gridcutoffsecondary double lowercut double uppercut Sets the lower and if supplied upper secondary cutoff values for the current grid For example gridcutoffsecondary 0 0014 sets the secondary lower grid cutoff for the current grid to 0 0014 leaving the upper secondary cutoff unchanged gridlooporder Syntax void gridlooporder string order Set the grid loop order to use with addnextgridpoint affecting in which order the dimensions of the data grid are filled order should be given as a string of three characters e g xyz equivalent to 123 yxz equivalent to 213 etc 190 For example gridlooporder zyx sets the loop order to the reverse of the default so that the z index is filled first gridorigin Syntax void gridorigin double x double y double z Sets the origin of the grid data in For example epa loro tal LO 10 sets the grid origin to be offset 10 along the y axis gridortho Syntax void gridortho double a double b double c Sets up an orthorhombic system of axes for the grid data For example ciclo Mea OoS Do sets up a system of axes elongated in the z axis gridstyle Syntax void gridstyle string style Determines how the current grid data is drawn on screen Valid styles are listed in Grid Styles Fo
59. drawn attached to an existing atom in a model the resulting bond length is adjusted to match the two elements involved if the Adjust Bond Length on Paste checkbox is ticked Fragment Models Fragment models are just normal models stored in specific places The only real difference is that atoms with unknown element integer 0 or string X X are slightly more useful than usual These can act as anchor points for the fragment that do not correspond to the position of any proper atom to allow for more control over the placement of structures for instance such an atom may be placed at the centre of a ring It is important to note that all atoms with unknown element type are removed when the fragment is added to the current model Anchor Points At any time a single atom in the selected fragment represents the attachment point and appears directly under the mouse pointer Any atom in the fragment can be selected as the 76 current anchor point and may be cycled through by pressing Alt If the atom acting as the anchor point has at least one bond to another atom then a reference vector is constructed allowing the fragment to be oriented along vectors dependent on the current geometry of existing atoms for example Placing Fragments in Free Space Single clicking in free space i e not over an existing atom places a copy of the current fragment in the current orientation in the current model Click dragging allows the fr
60. ee ee eee 131 9 1 A dns E a serene eines tiga tes ne 131 92 Bond Commands ss estiss lie dia 137 93 Buildg Commands A rada 141 DAS A hse toasts gies crate er as anal et A laacna stated 148 TN CES O e TE 153 90 Colourscales Commands eternas 155 9 7 Disorder Commands css ie ida 158 OS Edit Commands A A A tal cae 159 O Ener Gy COS ss 161 9 10 A 6 2h Ge eee BN Be ea Aes 165 Ol sPorceheldComimands Sia cas 170 9 12 Forces Commands A eaa eae Sola AE ath A Se vee Meee ag 180 23 Glyph Command Sunrise 181 9 14 Grid Commands vii das 187 9 15 Image Commands diia iaa ii 194 9 16 Labeling Commands ii ae 196 9 17 Math Commands pri ii a da 197 ONS r Measurine COM MOS O A A 200 9 19 Messaging Commands suis ir iii aia 203 9 20 Minimiser Commands 220 5203 05220 india 205 Ob Model Extras COMMON 207 O22 Model COMBINADAS 23 04 A A i Sh ge sen ee 209 9 23 Monte Carlo Commands tdt A A alsa lal stem tetas 215 9 24 Pattern Commiands vrien Bele ae A 217 O 25 Script Commands ii Goat eases a eet eee aed delle tae eae 229 0260 Selechon COMAS ita BAe A a AAA A A A ie aA 230 A A e ns acai cee cane see ee E as eatin Me 239 DDS Snes 241 929 O A A A Eaa EET 246 9 30 Trajectory COMO ind 249 9 31 Transform A eae hp can sca ee eaters alts 251 OSD View GC OMIM ANS co adecco da tale 258 10 TOpieS IE 262 10 1 Wolourscales o ade te is Ree ae eee ae cee 262 A E 263 10 33 O ES aS ee 264 A A cai a clad r
61. enclose certain atoms within solid structures There are two principal modes of operation The first the default assumes that the current atom selection consists of individual atoms that should be enclosed in a polyhedron made up from triangles 181 added between triplets of bound neighbours The carbon atom at the centre of methane would make a good example The alternative mode requested with the fragments option assumes that atoms within individual bound fragments in the current selection should be used as the vertices to form an enclosed shell Possible options are Option Effect centres Assume that the current selection consists of individual atomic centres that should be enclosed the default fragments Use individual bound fragments instead of assuming individual centres nolink Do not link the coordinates of generated glyphs to coordinates of the atoms the default is to link glyph coordinates to atoms rcut distance Specifies the maximum distance allowed between vertices of a triangle Autopolyhedra Method for a description of the process glyphatomf Syntax void glyphatomf int n void glyphatomf int n atom int sourceatom Set current or specified atom s forces as data n in the current glyph For example glyphatomf 1 links the current atoms forces to the first datum in the current glyph glyphatomr Syntax void glyphatomr int n void glyphatomr int n atom int sourceatom Set c
62. existing model Significantly the model may have existing contents which will be preserved during the build The second choice creates a new model for the system and a user input is required in order to define the cell dimensions These dimensions will act as a target for the builder The final choice creates a new model however the dimensions of the cell are not predetermined and are calculated by Aten depending on the number and density of the requested molecules as defined by the user The proportions of the cell may be set by the user The second step in the disordered builder defines the cell This screen will depend on the user choice for the first screen 1 User input required select model to be used as target 2 Define the length and angles for the target model 3 Define the length ratios and angles for a target model The absolute length of the final target model cell walls will be generated by Aten depending on the contents defined by the user 70 It is possible to select a partitioning scheme to apply to the cell This is only available for a pre existing model The possible partitioning options are None cylinder sphere and slab In step four the wizard provides a choice of components The models representing the components to be added to the target model may be selected In order to select multiple components hold shift and ctrl The final step in the disordered builder wizard sets the population of the compo
63. from these messaging commands is directed to either the GUI message box or stdout on the command line Formatted Output for explanations on the usage of C style formatted output Read Write commands for commands to read write from to files error Syntax void error string format Print a message to screen and immediately exit the current command structure filter For example baje ce ag Win aLilieene anule bacily Srror ki Win Sri notifies the user that something bad probably happened provided the error code and promptly exits printf Syntax void printf string format Standard printing command For example pala Mloacduncmedatarwne NANS prints the string Loading data to the screen printf Number of atoms i n natoms prints the contents of the variable natoms to the screen verbose 203 Syntax void verbose string format Prints a message but only when verbose output is enabled with the v command line switch For example verbose Extra information for you n 204 9 20 Minimiser Commands Perform energy minimisation on models cgminimise Syntax void cgminimise int maxsteps Geometry optimises the current model using the conjugate gradient method For example cgminimise 20 runs a conjugate gradient geometry optimisation for a maximum of 20 cycles Literature methods for details on the conjugate gradi
64. importing certain models which do not store element information Note that the keeptypes and keepnames switches are mutually exclusive M m lt name element gt map lt name element gt Manually map atom typenames occurring in model files to elements according to the rules defined here For example bob pe gt aten map CX C N P will result in atoms called CX being mapped to carbon and atoms called N_ mapped to phosphorus for whatever reason These mappings are attempted prior to any z mapping scheme defined in the filter and so will take precedence over standard typename to element conversions N 49 n Create a new empty model nobond Prevent recalculation of bonding in loaded models overriding filter directives This basically means that if a filter tries to run the rebond command then specifying nobond will prevent it nocentre Prevent translation of non periodic models centre of geometry to the origin overriding filter directives nofold Prevent initial folding of atoms to within the boundaries of the unit cell if one is present in loaded models overriding the use of the fold command in the corresponding filters nofragments Prevent loading of fragments from both standard and user locations on startup nofragmenticons Prevent generation of fragment icons used in the Fragment Library Window see Section 7 13 noincludes Prevent loading of global inclu
65. in a file which doesn t yet exist and which is referenced by the environment variable Sprofile You can type this into PowerShell and see exactly where it points to PS C Documents and Settings Your Name gt Sprofile C Documents and Settings Your Name My Documents WindowsPowerShell Microsoft PowerShell profile psl We must first create the directory where this file is expected to be PS C Documents and Settings Your Name gt mkdir My Documents WindowsPowerShell Directory C Documents and Settings Your Name My Documents Mode LastWriteTime Length Name el 23 04 2011 MOS WindowsPowerShel1l PS C Documents and Settings Your Name gt 1s My Documents Directory C Documents and Settings Your Name My Documents Mode LastWriteTime Length Name d ZA EOL 10 49 Downloads d r 10 07 2009 2859 abil My Music Gleie 08 04 2010 16335 My Pictures d AOS 772018 08 47 My Received Files d r 26 06 2010 19 44 My Videos d a 23 04 2011 ial FOS Windows PowerShell 23 04 2011 Ly eas 637740 glext h You can then create and edit the profile file directly with Notepad PS C Documents and Settings Your Name gt notepad Sprofile In the empty file paste the following into it and adjust any paths versions as may be necessary Setup Visual Studio and Windows SDK environment variables if test path path Senv VS100COMNTOOLS e
66. length Finally the Orthogonalise and Generate buttons allow particular axes to be orthogonalised relative to or generated from the other defined axes Matrix Conversion o x Atom Transform Source Target x Ez 0 00000 0 00000 Q y ozono 6 jroo 0 foomo G 0 00000 0 00000 0 00000 0 Jl Figure 7 37 Transform Window Matrix Convert page 91 It is possible to transform the orientation of a given set of atoms if a suitable pair of source and destination matrices are defined The Source matrix defines what should be considered the current frame of reference for the current set of coordinates Once the Convert button is pressed a rotation matrix is generated such that when applied to the Source matrix and the current atom selection it will be transformed into the Target matrix As for the matrix convert page the Pick Normalise Orthogonalise and Generate buttons allow each axis to be selected normalised orthogonalised relative to the others and generated from the others respectively 92 7 22 ZMatrix Window Matrix Window The z matrix window allows the z matrix for the current model to be viewed and its variables edited Any changes made are reflected immediately in the coordinates of the model Figure 5 29 ZMatrix Window 93 8 Command Language 8 1 Command Language Overview The scripting language in Aten is based syntactically on C C with ec
67. matrix for the glyph Note that not all glyphs can be rotated see the topic on Glyphs for more information selected int Whether the glyph is currently selected solid int e Specifies whether the glyph is drawn as a filled solid shape or in wireframe text string Text data associated to the glyph Not all glyphs use text type string Style of the glyph see Glyph Types Section 16 9 for a list visible int Flag indicating whether the glyph is currently visible 8 2 27 Glyph Type Functions recolour Syntax void recolour double r double g double b double a 1 0 Recolour all data vertices of the glyph to the specified RGB A value each component of which should be in the range 0 0 to 1 0 inclusive resetrotation Syntax void resetrotation Reset any rotation applied to the glyph rotatex Syntax void rotatex double angle Rotates the glyph by angle degrees about its x axis 111 rotatey Syntax void rotatey double angle Rotates the glyph by angle degrees about its y axis rotatez Syntax void rotatez double angle Rotates the glyph by angle degrees about its z axis 8 2 28 GlyphData Type The glyphdata type stores colour and position data for a single point in a glyph Table 8 17 GlyphData Type Members Member Type RW Description atom atom Atom if any from which positional data is retrieved atomdata int Type of data to retrieve from specified
68. model For example modelforces printforces Syntax void printforces Print out the forces of the current model For example printforces 180 9 13 Glyph Commands Add glyphs to atoms in the model autoellipsoids Syntax void autoellipsoids Note Experimental Feature Using the current atom selection this command creates ellipsoid glyphs that cover or represent individual bound fragments within the selection An ellipsoid glyph is added for each bound fragment within the selection positioned at the geometric centre of the bound fragment and scaled in an attempt to cover all atoms within the bound fragment Such things are useful when wanting to represent molecules by simple geometric shapes rather than by their fine grained atomic positions For instance given a box full of benzene molecules selectall autoellipsoids will add on a flattened ellipsoid to each individual molecule To do the same thing but using only the ring carbons to generate the ellipsoids select C autoellipsoids Now the ellipsoids will cover the carbon atoms in each ring leaving the hydrogens poking out Autoellipsoids method for a description of the process autopolyhedra Syntax void autopolyhedra string options Note Very Experimental Feature In a similar way to the autoellipsoids command autopolyhedra adds triangle glyphs to the current selection in an attempt to
69. model See the selectnone command for more details selecttree Syntax int selecttree atom i bond exclude NULL Select all atoms from atom i reachable by following any number of chemical bonds See the selectnone command for more details shiftdown Syntax void shiftdown int n 1 Shift the current atom selection down one or more places in the atom list towards higher IDs See the shiftdown command for more details shiftup Syntax void shiftup int n 1 121 Shift the current atom selection up one or more places in the atom list towards lower IDs See the shiftup command for more details showall Syntax void showall Unhides any hidden atoms in the model See the showa11 command for more details toangstroms Syntax void toangstroms Converts cell specification and atomic coordinates in the model from assumed units of Bohr into Angstroms No changes to associated trajectory frames or grid data is made torsionenergy Syntax double torsionenergy Calculates and returns the total torsion energy including improper terms for the current model transmute Syntax void transmute int string el Transmute all selected atoms to the specified element See the transmute command for more details undo Syntax void undo Undo the last change made to the model See the undo command for more details vdwenergy Syntax
70. monoclinic cell with 103 83 and side lengths a 11 854 b 2 904 and c 5 622 A You may want to zoom out afterwards to get a proper look at the new cell Define Open the Cell Define Window Add a unit cell to the model by checking the Has Cell Checkbox then go to the Define View ABC page and set the cell lengths a b and c to 11 854 2 904 and 5 622 respectively Set the cell angle f to 103 83 and click Define A Aten vL7 11671 Unnamed001 lt lt no filename gt gt Modified y YO File Edit View Selection Model Trajectory Forcefield Settings Scripts Help JBPAAA OY DA H eve MAREO Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click 0 Atoms 0 000000 g mol drag or rotate in local frame right click drag etri remove from selection Parallelepiped 0 000000 g cm Add Symmetry Unique Atoms There a five symmetry unique atoms to add into the cell which will in turn be used to generate the remaining 35 symmetry related atoms to give the complete unit cell To add the atoms we will use the Add Atom method in the editing tools available in the Build Window Atom positions in the paper are given in fractional coordinates we will create the atoms using these coordinates which will be converted to their real equivalents by Aten according to the current cell as we add them 23 Y Build In the
71. of controls on a different row Table 4 8 Layout Commands Option Value Description centre none By default all labels are right aligned so they sit next to their associated controls This forces the label to be aligned in the centre instead disabled none All controls are enabled by default Specifying disabled will gray out the control group name To place controls inside a groupbox instead of just adding them to the window the group property can be set For instance to add a control to a group box called 276 labelspan left newline parentspan span state tab ncols none none ncols ncols value name action page name Run Options you can specify group Run Options as an argument Note that the group name is displayed as the title of the group in the GUI If the named group box does not exist then it is created in the next available position i e after the last created control Otherwise the control is added to the existing group box in the next available position A label takes up a single column by default The label span property can be set to override this For example adding label span 4 to the list of arguments will force the label to span four columns instead of one By default all labels are right justified so they sit next to their associated controls This forces the label to be aligned to the left instead All controls are added to the immediate right of the last contr
72. or the b value on the Define View ABC page If you replicated the y direction by 2 0 earlier then the current value of b should be 11 238 Change it to 22 5 to roughly double the volume of the cell and create an interface in the xz plane Make a Water Model We will now create a water molecule in a separate model so we can add it in to the NaCl cell using the Disorder Builder Main Toolbar Create a new empty model if you don t have one already with L Build In the Build Window change the active element to oxygen on the Edit page by clicking M Select the draw single atoms tool Atom and click once somewhere in the empty model to create an oxygen Add hydrogens to the model by clicking Y AddH Model 29 A wy Aten vL7 11671 Unnamed002 lt lt no filename gt gt Modified Y YD Y File Edit View Selection Model Trajectory Forcefield Settings Scripts Help Dew AAA De RO e oaa Ram Eo Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click drag 3 Atoms 18 015000 g mol or rotate in local frame right click drag ctrl remove from selection Non periodic Add Water to the NaCl Cell It s time to run the disorder builder on the system We ll instruct the builder to add water in to the extended NaCl cell but only into the part which is empty 3 Disorder Run the Disorder Builder wizard g Disorder Wizard y Y
73. page Here we can mirror the coordinates of the current atom selection about its centre of geometry So mirror it once in any one of the x y or z directions or 2 Do not deselect the atoms afterwards since we still need to transmute them into chlorines Y Build On the Edit page in the Build Window set the current element to chlorine with fin Pick and then click 3 Transmute Sel A Aten vL7 1671 Unnamed001 lt lt no filename gt gt Modified Y YY File Edit View Selection Model Trajectory Forcefield Settings Scripts Help Vea AAA Se PR m eose Varese Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click 8 Atoms 233 772000 g mol drag or rotate in local frame right click drag etri remove from selection Cubic 388 187491 g cm Scale and Replicate Unit Cell We wish to scale the cubic unit cell of the model currently with side length 1 0 A to correspond to the unit cell of sodium chloride 5 628 A The cell can be scaled by a different amount in each Cartesian axis but since we want to end up with a cubic cell we must scale each axis by the same amount Once the model represents proper the basic sodium chloride unit cell we can replicate it to create a larger system Aten can replicate a basic cell by any integer or non integer amount along each of the three principal cell axes but here we will
74. required g cm3 setupcomponent both 1 100 1 483 Create a model with a basic unit cell the disorder builder will adjust its size as necessary newmodel box cell lO 0 130 90 90 90 disorder None FALSE Construct new forcefield using AMBER params newff chloroformff Un Taken from files at http www pharmacy manchester ac uk bryce amber Eyed CE O SS A COBRO RO RAE e on typedef 2 HZ HZ H amp 1 Chloroform hydrogen Do denr MOI MG LY SUIS Weno OEM ECNO ENSA abiceuctokese UALS A Oe SA y al O OS OSO 0 4 sO Al 0 0 src MI 2 0 2 SAO OST MATA OZONO 0 4 tarerzcsr Mie WO OS Ls USAS AO DIAZ 0 CL 50 6 0 ip bonddetiCintarmonsie sie Zi We tise2 CAN reali Ze alo Es bonddeHi wharmonwes EZ Gan SOA ARS 23 27 el DO ee angle dan o ica CALM SS iZ OS IMO 5 OS angled uha MOn ELY Mee UEM 50 LOS aL 3 finaliseff ffmodel Minimise our new system a little mcminimise 100 savemodel dlpoly chloroform CONFIG saveexpression dlpoly chloroform FIELD quit 39 5 8 Generating Images Without the GUI CLI Sometimes it s useful to quickly generate images for a system from the command line either because the system is prepared from the command line or because generating hundreds of images through the GUI is insanely repetetive To quickly save a picture of a system in it s standard view orientation i s as you would see it if you loade
75. same with respect to the force constant equilibrium distance etc So the forcefield will have to contain three intramolecular bond definitions covering CT H1 CT H2 and CT H3 each having the same parameters right Not necessarily While this is perfectly acceptable for large forcefields the number of redundant terms may become quite large and even for small forcefields with only a handful of terms adding in duplicate data might irk the more obsessive amongst us On these occasions atomtype equivalents can be defined which effectively link a set of atomtypes to a single identifying name that can then be used in any intramolecular parameter definitions In the waffle above aliasing the three hydrogens H1 H2 and H3 to a single typename H1 can be done as follows equivalents H1 B2 BG end Note that the aliased name does not have to be an atomtype name already defined in a types section function Syntax function type functionname argument list end The function block contains all the function definitions relevant to rule based forcefields Section 1 1 The function s should be written in the standard command language style Section 8 1 1 For example 297 function int generatebond ffbound data atom i atom j Calculate bond potential parameters between supplied atoms i and j data form morse return 1 end defines the function to be used when generation of a bond term is required
76. single bonds OF even 304 It s an oxygen atom with two hydrogens on it Given this degree level knowledge to describe the individual oxygen and hydrogen atoms in the grand scheme of the water molecule exactly you might say A water oxygen is an oxygen atom that is connected to two hydrogen atoms through single bonds And A water hydrogen is a hydrogen that is connected by a single bond to an oxygen atom that itself is connected by a single bond to another different hydrogen atom The extra information regarding the second hydrogen is necessary because otherwise we could apply the description of the water hydrogen to the hydrogen in any alcohol group as well Similarly we might mistake the oxygen in the hydroxonium ion H3O as being a water oxygen when in fact it is quite different In this case we could extend the description to A water oxygen is an oxygen atom that is connected to two hydrogen atoms through single bonds and nothing else An atom description in Aten is a string of comma separated commands that describe this kind of information So to tell the program how to recognise a water oxygen and a water hydrogen we could use the following type descriptions written in the proper forcefield input style for the types block il OW O nbonds 2 H H Water oxygen 2 HW H 0 nbonds 2 H H Water hydrogen Aten now recognises that a water oxygen OW is an oxygen atom that has exac
77. stick to integer amounts The Replicate method also allows specification of both negative and positive replication amounts for each direction Note that the values given in the Replicate page represent the total size which we require so input values negative positive of 0 0 0 and 1 1 1 will result in an unchaged cell g Transform On the Cell Transform Window go to the Scale page and enter a scale factor 28 of 5 628 for each of x y and z Press the Scale button to resize the unit cell Now select the Replicate page and enter positive replication values of 5 0 for both x and z and 2 0 for y and press Replicate to create the supercell A Aten vL7 r1671 Unnamed001 lt lt no filename gt gt Modified File Edit View Selection Model Trajectory Forcefield Settings Scripts Help JAR DY BA teoa a Wane O a O om a gt AR ee Nun Qe y Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle 400 Atoms 11688 600000 g mol click drag or rotate in local frame right click drag ctrl remove from selection Orthorhombic 2 177606 g cm Create an Interface It s a simple job to create an interface from the current system all we need do is increase the cell dimension along the y direction the cell s b length a Define Open the Cell Define Window and either change the central number of the Matrix page
78. sudan lle erario diana raid E ESE 330 Read SUCCESS NLC SEES sso arta O 331 A o Type Snare REN REO en OT ECO NE ee Mn ee e RR ee Rae ee 331 vi 1 Introduction 1 1 Overview Aten will let you generate and edit coordinates for your simulations and view any trajectories you might have generated A set of tools in the GUI and also accessible from the command line enables you to change the geometry of bonds angles and torsions translate atoms create atoms rotate groups of atoms and cut copy and paste them around the place All this can be done in the context of loading and saving in the format that you need 1f the file format you need isn t currently a part of Aten you yourself can write a filter to cover it Periodic systems are supported be they crystals liquids gases or a heady mixture All editing functions that are possible for simple molecules apply to periodic systems as well Moreover given a basic unit cell a whole crystal or a larger supercell can be constructed For any periodic system a random ensemble of molecules can be added allowing the facile creation of coordinates with which to begin your molecular dynamics simulations As well as coordinates Aten has support for forcefields in its own plain text format and can automatically apply these forcefields to your system if correct type descriptions are present for the atom types in the forcefield Then in the same way as with coordinates you may write out a for
79. than 0 1 A away from another selectoutsidecell Syntax int selectoutsidecell bool usecog FALSE Select all atoms whose coordinates are currently outside the confines of the unit cell if one exists If usecog is TRUE whole molecules are selected if their centre of geometry is outside the unit cell The number of newly selected atoms is returned For example int n selectoutsidecell selectpattern Syntax int selectpattern int id string name pattern p Selects all atoms in the current or named specified pattern Returns the number of atoms added to the existing selection For example selectpattern 2 236 select all atoms in the second pattern of the current model selectpattern bubble select all atoms in the pattern bubble of the current model selectradial Syntax int selectradial atom int id double r Select all atoms within r A of the supplied target atom which is also selected Returns the number of atoms added to the existing selection For example int nclose selectradial 10 4 5 selects all atoms within 4 5 of atom 10 and returns the number selected selecttree Syntax int selecttree atom int i bond exclude NULL Select all atoms which are reachable by following chemical bonds starting from and including atom i If a bond to exclude is provided then this connection will not be followed during the selection process
80. the newgrid command for more details paste Syntax void paste Paste the current clipboard contents into the model See the paste command for more details 119 rebond Syntax void rebond Calculate bonds in the model See the rebond command for more details rebondpatterns Syntax void rebondpatterns Calculate bonds within patterns in the model See the rebondpatterns command for more details rebondselection Syntax void rebondselection Calculate bonds in the current selection See the rebondselection command for more details redo Syntax void redo Redo the last undone change in the model See the redo command for more details reorder Syntax void reorder Reorder atoms so bound atoms have adjacent IDs See the reorder command for more details savebitmap Syntax void savebitmap string format string filename int width auto int height auto int quality 100 120 Save a bitmap image of the current model view See the savebitmap command for more details selectall Syntax void selectall Select all atoms in the model See the selectall command for more details selectionaddhydrogen Syntax void selectionaddhydrogen Hydrogen satisfy all atoms in the current selection See the selectionaddhydrogen command for more details selectnone Syntax void selectnone Deselect all atoms in the
81. used in calculation of the vdW interactions for a system For example wee 9 4 0 z sets the vdW cutoff radius to 9 0 A 164 9 10 Flow Commands Loops and if tests Flow control is styled to replicate the common syntax used in C Because of this providing an in depth explanation here is unnecessary since lots of people have already written far clearer and more in depth documents A good Google should find them do Syntax do commands while condition The do while loop is cousin of the for loop except that there is no control variable The termination of the loop depends on the condition which is tested at the end of every execution of the commands If the condition evaluates to TRUE the commands are executed again and condition re tested afterwards If FALSE the loop ends For example ine r I clo ak a amp Bp oroi Wa Bolla ao 4 ade Gk lt 00 will print out the following H H H H H H H hoe a To ah p md Note that the final value of i inside the loop is 128 greater than 100 since the condition is only tested at the end of the execution of the commands The while loop works in the same way save that the condi tion is tested at the beginning of the loop before commands are executed rather than at the end for Syntax for startvalue condition increment commands Three separate components make up a for loop startvalue defines both the control
82. using the cosine potential Ee OSLOMN SNC OS OMS SS SS SS MONZA cay Cr TO LO 2 0 On ds 0 Cu O Oss 1 4 0 defines two C C C 0 torsions of the triple cosine form and with custom scale factors types Syntax types typeid typename element NETA description 299 end The core of the forcefield file is the types section listing the ids names and elements of the different atom types present in the forcefield as well as a description telling Aten how to recognise them The typeid is an integer number used to identify the type It should be positive and must be unique amongst all those defined in a single forcefield typename is the actual name of the atom type OW C1 N_ar etc and is referred to in the other sections of the forcefield file and element is the type s element symbol as found in the periodic table 0 C N etc The string NETA defines how Aten should recognise this particular type in quotes if necessary optionally followed by a short text description of the type which appears in lists within the program to help identify particular types Atom types may be defined over multiple types blocks within the same file if necessary but while more than one types block may exist but all type IDs must be unique over all such blocks For example types 35 CT C nbonds 4 Simple tetrahedral carbon end describes a bog standard tetrahedral carbon called CT and assigns it an ID of 35 uaty
83. variables will likely be set to a value of zero or whatever passes for zero in the context of the type For all delimited writing operations a suitable standard format specifier is chosen with which to write out the data 11 3 8 Unformatted Reading and Writing TODO 287 288 12 Forcefields and Typing 12 1 Overview If you re doing anything interesting with a model or a molecule a suitable forcefield description of the system is a must A forcefield contains lists of parameters that describe the interactions between atoms for example bonds angles and van der Waals interactions More specifically a forcefield contains parameters to describe many such interactions in many different types of molecule or chemical environment An expression referred to throughout the manual should be thought of as the subset of terms from a given forcefield necessary to describe all the interactions within a model Aten has its own free format for forcefield files described in the following sections Once loaded in the energy and forces in Models can then be calculated and allows energy minimisation etc More so once a set of forcefield parameters has been read in and used to describe a model this expression can be written out using a custom format ready for input into something else 12 1 1 File Format The basic forcefield file format is designed to be as readable as possible by both machine and user Lines are free format mea
84. water script loaded in the previous example 229 9 26 Selection Commands Select atoms or groups of atoms within the current model deselect Syntax int deselect atom int string selection Deselect atoms in the current model returning the number of atoms deselected by the provided selection arguments One or more arguments may be supplied and each may be of the type int atom or string In the case of the first two types individual atoms or those corresponding to the integer id are deselected On the other hand strings may contain ranges of atom IDs and element symbols permitting atoms to be deselected in groups Ranges are specified as a b where a and b are either both atom IDs or both element symbols In addition the symbol can be used before a or after a an atom ID or element symbol to mean either everything up to and including this or this and everything after Within a string argument one or more selection ranges may be separated by commas For example deselect 5 deselects the 5th atom deselect 1 10 N deselects the first ten atoms and all nitrogen atoms int n deselect Sc Zn deselects the first transition series of elements returning the number of atoms that were deselected in the process deselect Ct deselects all elements carbon and above ceselear ll 2 5 VE deselects the first second and fifth atoms as well as the eighth
85. 0 degrees around the x axis 259 speedtest Syntax void speedtest int nrenders 100 Performs a quick speed test based on rendering of the current model and general view For example speedtest spins the current model for the default of 100 rendering passes speedtest 2000 spins the current model for 2000 rendering passes translateview Syntax void translateview double x double y double z Translates the camera viewing the current model For example translateview 0 0 0 0 1 0 viewalong Syntax void viewalong double x double y double z Sets the current view so that it is along the specified vector For example viewalong 0 0 1 view the current model along the negative z axis viewalongcell 260 Syntax void viewalongcell double x double y double z Sets the current view so that is along the specified cell vector For example viewalongcel1 1 0 0 view the current model along the cell s x axis zoomview Syntax void zoomview double dz Zooms the view by the specified amount For example zoomview 10 0 moves the camera 10 A forwards along the z direction zoomview 5 moves the camera 5 A backwards along the z direction 261 10 Topics of Interest 10 1 Colourscales TODO 262 10 2 Glyphs A glyph in Aten is any of a series of primitives or shapes or objects that can be re
86. 0p k2 k3 Cosine 23698 UQ 12k 1 cos npeq cos np Product B a peq Dreiding dreiding UQ 12k l cos n Peq k Cosine j peq 319 14 External Programs TODO 14 1 Movie Generation 14 2 MOPAC 320 15 Methods Some things in Aten are implemented from existing routines and algorithms Some have been written from scratch even when existing algorithms were available either as an attempt to improve those existing algorithms or simply to learn more by working out how best to go about solving a given problem A selection of algorithms are detailed in the following pages grouped into those that were re used from the literature and those that were written specifically for Aten It should be pointed out that in the eventuality that somebody notices that one of Aten s custom algorithms is actually a reproduction of an existing method then fair enough send me the reference and I ll be happy to move it to the proper section 15 1 Custom Algorithms 15 1 1 NETA NETA stands for the Nested English Typing Algorithm a fairly dull acronym all said and done but with the advantage that it is Aten backwards NETA is an attempt to provide a descriptive atom typing language that is e Easily readable e Easily written from a small subset of keywords e Recursive and able to describe complex molecules It s closest relative that I m aware of in the literature is the ATDL as implemented in Vega ZZ 1 but wa
87. 1 makes the first atom in the current model the current atom and returns a reference to it fix Syntax void fix atomlid id 0 131 Fix the positions of the current atom selection or individual atom specified so that they remain in the same position following various methods e g minimisations For example fix fixes the positions of all selected atoms EOE E lt A A e fixes the positions of the first 10 atoms in the current model free Syntax void free atomlid id 0 Free the positions of previously fixed atoms in the current selection or the individual atom specified For example free 5 allows the fifth atom in the current model to be moved again getatom Syntax atom getatom atomlid id Return a reference to the atom specified For example atom i getatom 3 returns a reference to the third atom in the current model hide Syntax void hide atom id id 0 132 Hides the current selection of atoms or the supplied atom from view meaning they cannot be selected by direct clicking highlighting in the GUI They are still subject to transformation if they are selected by other means For example select H hide selects and hides all hydrogen atoms in the current model setcharge Syntax void setcharge double q void setcharge double q int id Set the atomic charge of the current or specified atom
88. 142 locate Syntax void locate double x double y double z Sets the pen position to the coordinates specified in A For example Locara 0 0 DO DO moves the pen back to the coordinate origin move Syntax void move double x double y double z Moves the pen position by the amounts specified in A For example niower 1l WO OA ON moves the pen one A in both the positive x and y directions movetoend Syntax void movetoend Move the current atom selection to the end of the list The relative order of atoms in the selection is preserved For example movetoena movetostart Syntax void movetostart 143 Move the current atom selection to the start of the list The relative order of the atoms in the selection is preserved For example movetostart newatom Syntax void newatom int string el void newatom int string el double x double y double z void newatom int string el double x double y double z double vx double vy double vz void newatom int string el double x double y double z double vx double vy double vz double fx double fy double fz Create a new atom of element e1 at the current pen position or if provided the specified coordinates and optional velocities or velocities and forces Either the integer atomic number or the symbol name of the element may be used to identify th
89. 15 1 3 Autoellipsoids TODO 323 15 1 4 Autopolyhedra TODO 15 1 5 Rebond The most common means of determining connectivity between a collection of atoms is based on simple check of the actual distance between two atoms and the sum of their assigned radii img align center src show_image php id 116 stk We stk WS The two sigma s represent the radii of atoms i and j which have coordinates xi yi zi and xj yj zj The parameter alpha is an adjustable tolerance value to enable fine tuning and using Aten s set of built in radii 1 usually lays between 1 0 and 2 0 For molecules or periodic systems of modest size the method can be used as is but for large systems of many atoms the use of a double loop over atoms results in a very slow algorithm Aten overcomes this slowdown for larger systems by partitioning the system up into a series of overlapping cuboids For a system of N particles in a periodic box or an isolated system with an orthorhombic pseudo box determined by the extreme positions of atoms the volume is partitioned into a number of subvolumes of some minimum size in each direction The minimum size of any one of the subvolume s dimensions is chosen relative to the maximum bond length possible given the largest elemental radius and the current bond tolerance alpha A single loop over atoms is then performed to associate them to these subvolumes Each atom belongs to at least one cuboid determine
90. 33 see declaration of getenv Linking CXX executable bin Aten exe 100 Built target Aten PS C Documents and Settings Your Name My Documents aten 1 7 1626 gt If this is what you see then you ve built Aten successfully You ll need to point Aten to it s data directory by hand From the command line you can run the following PS aten 1 7 1626 gt bin Aten exe atendata data You can also set up a shortcut to the executable and set the option there 2 3 10 Potential Readline Errors There is the potential for the build to fail on the basis of odd readline errors C Program Files GnuWin32 include readline keymaps h 97 see declaration of rl_set_keymap C Program Files GnuWin32 include readline readline h 364 error C2375 Viel ger kemeo recerinicion Calcio C Program Files GnuWin32 include readline keymaps h 94 see declaration of rl get _keymap NMAKE fatal error U1077 C PROGRA 1 MICROS 1 0 VC bin cl exe return code OZ Stop NMAKE fatal error U1077 C Program Files Microsoft Visual Studio 10 0 VC BIN nmake exe return code 0x2 Stop NMAKE fatal error U1077 C Program Files Microsoft Visual Studio 10 0 VC BIN nmake exe return code 0x2 Stop PS C Documents and Settings Your Name My Documentslaten 1 7 1626 gt 10 These errors arise because the functions r1_ _ are declared differently between the readline h and keymaps h header files but
91. 4 Standard tetrahedral carbon creates a new simple type for a carbon atom with four bonds typemodel Syntax int typemodel Perform atom typing on the current model Returns 1 if atom typing was performed successfully or 0 otherwise For example int success typemodel typetest Syntax int typetest int typeid atom int id Test the current forcefield s atomtype typeid on the atom specified returning the type score of the match zero indicating no match For example 178 int score typetest 112 10 tests typeid 112 on the tenth atom in the model units Syntax void units string unit Sets the units in which energetic parameters are given for the current forcefield For a list of available units see energy units vdw Syntax void vdw bool calculate Controls calculation of van der Waals terms in energy force calculations on by default For example POW UOTE turns van der Waals energy force calculation off vdw TRUE gt turns van der Waals energy force calculation on 179 9 12 Forces Commands Calculate forces for models and trajectory frames frameforces Syntax void frameforces Calculate the atomic forces of the current frame of the trajectory associated with the current model For example frameforces modelforces Syntax void modelforces Calculate the atomic forces of the current
92. 5 Lock Y 0 000000 JO Lock Z 0 000000 Lock 7 Define Laniro Figure 7 28 Position Window Centre page The Centre page allows the centre of geometry of the current selection to be positioned at absolute coordinates The desired position is entered in the three input boxes or can be defined from the geometric centre of a selection of atoms prior to the positioning of a different set Any or all of the Cartesian axes may be locked preventing coordinate adjustment along particular directions Position o x Centre Flip Translate Shift Reposition ke Figure 7 29 Position Window Flip page The Flip page mirrors the positions of atoms in the current selection through its centre of geometry in either the X Y or Z directions Note that this tool currently works only along the Cartesian axes and does not take into account the shape of any defined cell 84 Position o x Centre Flip Translate Shift Reposition Frame Model lt be E World _ Wor e y m Cell Shift 1 00000000 lt gt Figure 7 30 Position Window Translate page Translations of atoms within model local world view and cell frames of reference can be performed in the Translate page The group of directional buttons move the selected atoms along the relevant axis within the selected frame of reference and by the amount specified in the Shift control For model and world reference frames the Shift control specifi
93. E This is related to the version of pkg config you have installed e g version 0 15 1 gives this error but version 0 21 does not with Fink MacPorts Upgrade to the latest version Incidentally the line number reported 16 is not the actual location of the error autoconf reports this wrongly the actual error occurs later on with the PKG CHECK MODULES GTK28 AC DEFINE command OSX Warning Underquoted definition of PKG_CHECK_MODULES Running autogen sh aclocal complains sw share aclocal pkg m4 5 warning underquoted definition of PKG_CHECK_MODULES If pkgconfig is not installed this is likely to give rise to the said spurious error Install pkgconfig from Fink MacPorts to proceed ALL autogen sh appears successful but aclocal complains about underquoted definition of AM PATH These warnings should not have affected the generation of a working configure script So you may as well move on to the next step in the build 3 2 Compilation Errors ALL Error uic File generated with too recent version of Qt Designer 4 0 vs 3 x x This error can occur when both the Qt3 and Qt4 development packages are installed The SPATH is sometimes set so that the Qt3 binaries are found first so the Meta object compiler from Qt3 is called and then the generated source includes the Qt4 headers Running which moc will tell you which binary is being used you can then run this binary with the v option to che
94. Keyword Examples Command Meaning ch in C C 0 0 Specifies a minimum four carbon chain of any 311 degree of saturation chain C nh 2 C nh 2 Explicity specifies an all atom butyl chain C nh 2 C nh 3 n The n keyword when placed in the bracketed parts of bound atom ring and chain descriptions requires that they are matched a number of times rather than just once Table 12 7 NETA n Keyword Examples C n 4 H n 3 Describes the central carbon in neopentane 2 2 dimethylpropane which is bound to four methyl groups ring size 4 n 3 Specifies that the target atom should be present in three unique four membered rings chain C C C N bond triple n 4 Requests that the atom has four cyanoethyl groups hanging off it nbonds nbonds specifies the exact number of connections that an atom must possess Table 12 8 NETA nbonds Keyword Examples Command Meaning nbonds 2 Demand that the atom has exactly two connections N nbonds 1 Describes a nitrogen with only one bond perhaps an sp1 nitrogen with a triple bond nh The nh keyword is shorthand for explicitly specifying the number of attached hydrogens to the target atom or a bound atom It is equivalent to stating H n m Table 12 9 NETA nh Keyword Examples Command Meaning C nh 2 Atom is bound to a methylene carbon with exactly two hydrogens on it aromatic 312 aromatic indicates either that an atom must b
95. Only functions with certain names will be recognised and used properly by Aten See the functions section 12 4 1 in rule based forcefields for more information and a list of valid function declarations that may be made generator Syntax generator type name The generator block is defunct as of code revision 1267 Use the data block instead inter Syntax inter form typeid typename charge datal data2 end Intermolecular van der Waals parameters and the charge associated with each atom type belong in the inter section There may be multiple inter sections within the same forcefield file but parameters for an individual atomtype may be defined only once The inter keyword begins a block of intermolecular parameter definitions and the single argument form should specify the functional form of the intermolecular interactions contained within typeid and typename refer to a single type defined in a types section charge is the atomic charge of this atomtype and then follows the data describing the interaction The order of the values given should correspond to the order of parameters expected for the specified functional form see Section 13 1 for a list of valid forms and their parameters For example the Lennard Jones potential takes two parameters epsilon and sigma in that order For a chloride atomtype with ID 24 if epsilon 0 5 sigma equals 3 0 and the charge on the atomtype is
96. Read a line of delimited items from the input file placing them into the list of variable s provided Conversion of data from the file into the types of the destination variables is performed automatically The number of items parsed successfully is returned For example double x y z int n readline x y z reads a line from the file and places the first three delimited items on the line into the variables x y and z readlinef Syntax int readlinef string format Read a line of data from the input file and separate them into the list of variable s provided and according to the format provided The number of items parsed successfully 1s returned For example double x y z int n readlinef 8 6f 8 6f 58 6f x y Z reads a line from the file assuming that the line contains three floating point values of 8 characters length and separated by a space into the three variables x y and z readnext Syntax int readnext int i int readnext double d int readnext string s Read the next delimited argument from the last line read with either getline or readline into the variable supplied The command returns either TRUE for success or FALSE e g if the end of file was reached without reading any non whitespace characters or an error was encountered For example 224 double d int n readnext d read the next delimited argument into the double variable d readvar S
97. Selection Atom selection or picking is performed with the left mouse button by default single click on any atom to highlight select it Single clicks perform exclusive selections that is all other atom s are deselected before the clicked atom is re selected Clicking in an empty region of the canvas deselects all atoms Clicking on an empty space in the canvas holding and dragging draws a rectangular selection region releasing the mouse button then selects all atoms within this area Again this selection operation is exclusive Inclusive selections where already selected atoms are not deselected are performed by holding the Shift key while performing the above operations Furthermore single clicking on a selected atom while holding Shift will deselect the atom 56 7 3 Keyboard Shortcuts Shortcut Action Escape Box Select Ctrl A Select All Ctrl C Copy Ctrl Alt C Centre Selection Ctrl D Deselect All Ctrl Delete Delete Ctrl F Fold Atoms Ctrl Shift F Fold Molecules Ctrl H Hide Selection Ctrl Shift H Show All Atoms Ctrl I Invert Selection Ctrl N New Ctrl O Open Ctrl P Play Pause Ctrl R Reset View Ctrl S Save Ctrl V Paste Ctrl X Cut Ctrl Y Redo Ctrl Z Undo Ctrl 1 Stick Ctrl 2 Tube Ctrl 3 Sphere Ctrl 4 Scaled Ctrl 5 Individual Ctrl Zoom Out Ctrl Zoom In Ctrl Alt lt First Frame Ctrl Alt gt Last Frame Ctrl Right Next Model F8 Detect H Bonds F10 Quick Command Description Return to ba
98. The z depth at which binned transparency sorting begins Before this value all triangles are grouped and rendered together without sorting Colour of unit cell axis pointers Colour of unit cell Whether to use the grabFrameBuffer usenicetext vdwcut vibrationcolour viewrotationglobe warn1056 zoomthrottle method of the main widget instead of the normal renderPixmap method when saving bitmap images If saving an image results in a completely black or corrupt bitmap try setting this to TRUE int Whether QPainter on 1 TRUE or QGIWidget off 0 FALSE is used to render label text double The VDW cutoff distance double 4 Colour of vibration vector arrows int Whether to draw a rotation globe in the lower right hand corner for each model int Many changes to the typing language syntax were introduced in revision 1056 and a warning message was implemented This can be turned off by setting this variable to FALSE double e Zooming throttle value used to calm down or increase the distance jumped when zooming with the mouse 8 2 36 Site Type Table 6 38 Site Type Members Member Type RW Description 8 2 37 UnitCell Type The unitce11 type contains a full unit cell specification for a model including any associated spacegroup Table 8 23 UnitCell Type Members Member Type RW Description a doubl alpha doubl b doubl beta doubl c doubl ax doubl ay doubl az doubl bx doubl by dou
99. We may then define a default value for this argument such that if the function is called without it this default value will be assumed WOLLC cest ovce de ab lie aj cloulole ataciror 10 0 Ll son y parate VCalline meesiras Lane int num 2 testroutine num 4 testroutine num 4 20 0 PENA MV IDYoyaress Nua Both methods of calling testroutine in this example are valid 8 1 8 Return Values 98 For functions defined to return a specific type at some point in the body of the function a suitable value should be returned This is achieved with the return keyword Consider this simple example which checks the sign of a numeric argument returning 1 for a positive number and 1 for a negative number int checksign double num ae inetd lt lt 0 recia Lp else return 1 If an attempt is made to return a value whose type does not match the type of the function an error will be raised Note that once a return statement is reached the function is exited immediately For functions that do not return values 1 e those declared with void then return simply exits from the function no return value need or should be supplied 8 1 9 Arithmetic Expressions and Operators Arithmetic operates in the same way as in C and utilises the same operator precedence etc Similarly comparison operators less than equal to etc are the same as those found in C 99 8 2 Variable Types 8 2 1 Overview For variabl
100. Zhang F Huo Z Liu W Wang W Shi and E J Maginn J Phys Chem B 113 7591 7598 2009 o Z Liu X Wu and W Wang Phys Chem Chem Phys 8 1096 1104 2006 12 3 Keyword Reference 12 3 1 General Keywords General keywords are simple keywords that take single items of data as arguments name Syntax name name of forcefield Sets the name of the forcefield as it appears in the program For example name Test Forcefield sets the name of the forcefield to Test Forcefield units Syntax units energyunit Specifies the units of energy used for energetic forcefield parameters Any energetic parameters specified in the forcefield are converted from the units specified here into the internal units of energy once loading of the forcefield has completed 293 For example units kcal indicates that any energetic values supplied in the forcefield are in kilocalories per mole convert Syntax convert name Only relevant if a data block exists the convert keyword takes a list of parameter names defined in the data block s and marks them as being or containing a unit of energy When Aten converts between energy units these marked parameters will be converted also For example CONV Dig eeCuSe po indicates that the defined data variables Dij and e_sep are energy based and should be converted when necessary 12 3 2 Block Keywords All lists of terms types and extraneous data
101. a FIELD setcombinationrule Syntax void setcombinationrule string form string parameter string rule Sets the combination rule to use for the specifed parameter of the given functional form The formand related parameter should correspond to those given in the VDW functional forms table while rule should correspond to one of the available combination rule options For example setcombinationrule 13 sigma geometric torsiondef Syntax void torsiondef string form string type i string type j string type k string type 1 double datal 177 Add a torsion definition to the current forcefield form should correspond to one of the implemented torsion functional forms while the four types refer to either type or equivalent names of defined atom types Up to ten real valued parameter values for the function may be provided typedef Syntax int typedef int typeid string name string equiv stringlint element string neta string description Add a new atom type definition to the current forcefield with the identifying typeid and called name with the equivalent typename equiv The basic element of the new type is given as element and neta is the NETA definition of the type An optional string describing the type in more detail can be given in description The command returns 1 if the model was typed successfully or 0 otherwise For example typedef 101 Ctet C nbonds
102. a filters on Linux Mac or C Program Files Aten N MMM on Windows and copy this to your user filter directory On Linux Mac this is aten filters while on Windows this will be a directory called aten in your user home in Documents and Settings Rename your copy of the file to xyzbohr To make this new filter file read and write in units of Bohr we need to simply divide or multiply by 0 5292 depending on whether we re writing or reading the coordinates SO begin by changing the importmode1 section around line 23 to read LS merecia Teo S292 TO DAA ea DAA 2 So this just converts the units of Bohr in the file to Angstroms on input right The exportmodel section must be modified as well around line 38 for atom i m atoms i 0 1 writelinef 8s 12 6f 12 6f 12 6f MENA al O GED ak O ADA y al ic A ak sep p The importtrajectory section can be modified in a similar way or can be removed if it is not required As it stands this new xyzbohr filter will hide the original xyz filter since both the nicknames and IDs are the same and so they must be changed in the importmodel and exportmodel headers and the importtrajectory if it is still there Simply changing all occurrences of xyz to something like xyzb is enough as well as choosing an ID for the new filter which is not currently in use something above 100 is safe The next time Aten is run the user filter directory will be searched and the new xyzboh
103. agment to be freely rotated about the anchor point before the placement is final On placement the anchor atom is pasted too unless it is of unknown element see above Attaching to Existing Atoms When moving over an existing atom with an anchor point that has at least one bond to another atom the fragment is attached at a suitable geometry provided the valency of the atom allows if not the atom will be surrounded by a crossed out box and the fragment will temporarily disappear A single click will place the fragment in the shown position and orientation while click dragging rotates the fragment about the newly formed bond to allow fine adjustment before the final placement If the anchor point has no bonds to other atoms the fragment is placed in no specific orientation and click dragging freely rotates the molecule about the anchor point In both cases the anchor atom is always removed when being added to the model since the existing atom which was clicked on will replace it in terms of position If the existing atom in the model has one or more other atoms attached to it holding Shift will orient the fragment along an existing bond vector In this case both the anchor atom and the atom at the other end of the bond are removed when the fragment is placed Pressing Ctrl cycles over the bonds of the existing atom 11 7 14 Geometry Window Simple measurements of distances angles and torsions between picked atoms or the current sel
104. aining comments are automatically skipped stripbrackets Normal parentheses are automatically stripped from the input file noescapes Treat backslash as a normal character 330 16 15 Read Success Integers Integer return values for many read write operations Table 16 15 Read write return values 1 Success no errors encountered 0 The read write operation failed before it was completed al End of file was encountered during read operationll 16 16 ZMapping Types Table 16 16 Map type keywords Value Description alpha Convert based on the alpha part of the name only Leading or trailing numbers and symbols are discarded The alpha part is assumed to be an element symbol auto Attempts several of the other conversions of increasing complexity until a match is found ff Search through the names of atomtypes in currently loaded forcefields assigning elements based on matches found firstalpha Convert based on the first alpha part of the name only i e until a non alpha character is found The alpha part is assumed to be an element symbol name The name is assumed to be an actual element name and is converted to the relevant element number numeric Use the numeric part of the name as the element number singlealpha Convert based on the first alphabetic character encountered useful only when single character element symbols are likely to be found e g for pure organic CHON systems 331 batch processing 46 47 51 52 Comm
105. ajectory file is then rewound to the end of the header section start of the frame data One of two things then happens Since trajectory files are typically enormous hundreds or thousands of megabytes then it is unwise to try and load the whole trajectory into memory at once Aten knows this and from the estimated frame size also knows roughly how big the whole trajectory is If the total trajectory file size is greater than an internally defined limit the trajectory cache size then only a single frame is stored at any one point If the total size is smaller then this limit the whole trajectory is cached in memory Both have their advantages and disadvantages as listed in the following sections Uncached Frames If the trajectory is too big to be stored in memory Aten only holds a single frame in memory at any one time This means that e Memory use is minimised since only a single frame is loaded at any time e Performance is slower moving between frames means data must be read from disk e Edits are forgotten changes both atomic and stylistic made to the loaded frame are forgotten when a different frame is read Aten tries to minimise the seek time between frames by storing file offsets of frames it has already read in However since trajectory frames can be different sizes Aten never tries to jump ahead in the file based on the size of a single frame Skipping immediately to the final frame in the trajectory will thu
106. and Line Switches atendata 45 b 45 batch 46 bohr 45 bond 46 c 46 cachelimit 46 centre 47 command 46 d 47 debug 47 double 47 export 47 exportmap 47 expression 48 f 48 ff 48 filter 48 fold 48 format 48 g 48 grid 48 h 48 help 48 332 1 48 int 49 interactive 48 k 49 keepnames 49 keeptypes 49 keepview 49 m 49 map 49 n 50 nobond 50 nocentre 50 nofold 50 nofragmenticons 50 nofragments 50 noincludes 50 nolists 50 nolists 50 nopack 50 nopartitions 50 nogtsettings 50 pack 51 pipe 51 process 51 quiet 51 s 51 script 51 string 51 t 51 trajectory 51 u 51 undolevels 51 v 51 vbo 52 vbo 52 verbose 51 Z 52 zmap 52 Command Line Switches 51 commands abs 197 addframe 249 addgridpoint 187 addhydrogen 141 addnextgridpoint 187 addpoint 155 addreadoption 219 adjustcell 148 afterstr 241 angledef 170 atof 241 atoi 241 333 atomstyle 131 augment 137 autoconversionunit 170 autoellipsoids 181 autopolyhedra 181 axisrotate 251 axisrotateview 258 beforestr 242 bohr 141 bonddef 170 bondtolerance 137 cell 148 cellaxes 148 centre 252 cgminimise 205 chain 142 charge 153 chargeff 153 chargefrommodel 153 chargepatom 154 chargetype 154 clearbonds 137 clearcharges 154 cleare
107. and S Alvarez Dalton Trans 2008 DOI ihttp dx doi org 10 1039 b801115 324 15 2 Literature Methods The following table lists common literature methods implemented in Aten noting any implementation differences etc Table 15 1 Literature Methods Name Description Notes Ewald Sum Electrostatic energy and forces for periodic systems Implemented as described in XXX Conjugate Gradient Marching Cubes Isosurface generation from regular gridded data No pathological cases are accounted for See implementation details in XXX Steepest Descent 325 16 Enumerations The following tables list sets of keywords relevant to various data e g bond types to be used when setting or checking such values 16 1 Basis Shell Types A list of recognised types of basis shell recognised by the basisshel1 type Table 16 1 Basis shell type keywords Value Description nCartesians S Standard S shell Combined S P shell Standard P shell Standard D shell Standard F shell UU DE ZA UU 16 2 Bond Types A bond between atoms is of one of the following types Table 16 2 Bond type keywords Value Description any Special case never assigned to an actual bond but used in bond matching functions single A single bond double A double bond triple A triple bond aromatic An aromatic bond assigned automatically by the atom typing routines 16 3 Bound Types Possible intramolecular bound interaction types are
108. and there are plenty of filters already written to use as worked examples When a filter is called in order to write out data no references to any of the current 1 e displayed or selected data are sent directly to the filter itself Instead this must be probed by using the aten master reference available to all scripts commands and filters Within aten the currently displayed model may be deduced as well as the current frame if a trajectory is associated In most cases for model export filters the path aten frame should be used to determine the model data that should be written 11 1 1 Filter Contents A filter is a plain text file containing one or more C style programs that permit the input or output of data in a specific format For example a purely model oriented filter file may contain two filters one to read in files of the specified format and one to write the data out again Each individual filter is given a short nickname a shell style glob and possibly several other bits of data that allow files to be recognised if the file extensions defined for it are not enough Different filters that recognise the same file type may be provided if necessary each performing a slightly different set of import or export commands if it is not convenient to do so within a single filter and all will appear in the drop down list of filters in file dialogs within the program Note that in batch command line or scripting mode filter
109. application may Fix this problem This descriptive message suggests that the installation process failed but this is not the case The real reason for Aten s failure is that your machine lacks the Visual Studio C 2008 runtime libraries These can be freely downloaded from Microsoft s website http www microsoft com downloads en details aspx familyid a5Cc84275 3b97 4ab7 a40d 3802b2af5fc28displaylang en Allternatively search the internet for Microsoft Visual C 2008 Redistributable Package SP1 Note that it must be the Service Pack 1 version 14 4 Quickstart The following sections give an overview of the most important things to know about Aten It s only a few pages long and its well worth taking five minutes to read it 4 1 Terminology It is useful to know exactly what a few terms mean in Aten s world Model A model is a single molecule a snapshot of an ensemble of molecules in a liquid a crystal s unit cell basically any collection of atoms and bonds optionally including a unit cell definition and or a number of glyphs annotations or shapes Pattern A system containing many molecules can be described and manipulated efficiently through the recognition that there are sets of molecules of the same type A pattern describes one such set of similar molecules and a model s pattern definition may contain many individual patterns Many operations in Aten require that a pattern definit
110. arch for in the file If the string is found the file is identified as being readable by this filter type The number of lines searched is governed by the within property type Defines the kind of filter that is described i e if it loads saves acts on models grid data etc so that Aten knows when to use it Must always be defined within Specifies the number of lines to search for any supplied search strings zmap Determines which zmapping style to employ when converting atom names from the file exact Syntax YA exact namel name2 Occasionally and annoyingly files have no extension at all instead having short fixed names which must be checked for literally when probing files This command defines one or more explicit filenames that identify files targeted by this filter Multiple names may be given separated by commas or whitespace Exact filename matching is case insensitive For example exact coords associates any file called coords to this filter exact results output associates any files called results or output to this filter extension Syntax 269 extension extensionl extension2 Sets the filename extension s that identify files to be read written by this filter When files are being probed for their type in the first instance the filename is examined and the extension everything after the last is compared to those defined in filter sections by this
111. arly 150 replicate 0 0 0 4 4 4 replicare 2 2p Ar Lp Qe DQ F will both create a 5x5x5 arrangement of the original cell removecell Syntax void removecell Clears any cell description removes periodic boundary conditions from the current model For example removecell scale Syntax void scale double x double y double z bool calcenergy FALSE Scale unit cell and its constituent atoms by the scale factors x y and z The optional calcenergy parameter calculates the energy difference resulting from the scaling operation For example Scale lO 2 0 1 0 doubles the length of the y axis of the system x and z axes remain unchanged scalemolecules Syntax void scalemolecules double x double y double z bool calcenergy FALSE Scale unit cell and centres of geometry of molecules within it by the scale factors x y and z Within individual molecules the relative distances between atoms stays the same but the centres of geometry of other molecules do not The optional calcenergy parameter calculates the energy difference resulting from the scaling operation For example scalemolecules 0 5 0 5 0 5 151 halves the lengths of all axes scaling the positions of the molecules to reflect the new size setcell Syntax void setcell string parameter double value Set a single unit cell parameter one of a b c alpha beta gamma or one of
112. atic scaling factor between atoms 1 and 4 form string Functional form of intramolecular potential see the Section 13 for lists of allowable functional forms for each intramolecular interaction type natoms int Number of atoms involved in the bound interaction nparams int The number of parameters used by the functional form of the interaction type string Actual type of the bound interaction bond angle etc typenames string Names of the atom types the interaction is relevant to vscale double For torsion type interactions the VDW scaling factor between atoms 1 and 4 8 2 23 FFBound Type Functions parameter Syntax double parameter string name Search for and return the value of the parameter name within the bound interaction 8 2 24 Forcefield Type The forcefield type stores a complete set of atom types and ffbound interaction data Table 8 15 Forcefield Type Members Member Type RW Description energygenerators int Array of integers flagging which generator data are energetic and should be converted filename string Filename if the forcefield was loaded from a file name string Name of the forcefield nangles integer Number of angle terms defined in the forcefield natomtypes integer Number of atomtypes defined in the forcefield nbonds integer Number of bond terms defined in the forcefield nimpropers integer Number of improper dihedral terms defined in the forcefield ntorsions int
113. ation symbol string Atomic symbols of the element 8 2 19 EnergyStore Type The energystore type stores the last set of energy values calculated for a model or frame Table 8 12 EnergyStore Type Members Member Type RW Description angle double Total angle energy bond double Total bond energy electrostatic double Total electrostatic energy efrom Coulomb or Ewald sums torsion double Total torsion energy total double Total of all energy components ureybradley double Total Urey Bradley energy vdw double Total van der Waals energy 8 2 20 FFAtom Type The atom type stores parameter data relevant to a specific atom type in a forcefield Table 8 13 FFAtom Type Members Member Type RW Description charge double Charge associated to the type data double 6 Parameter data for short range potential datakeyword string Keyword names of the associated parameters up to nparams datanames string Proper names of the associated parameters up to nparams description string Text data describing the type equivalent string Equivalent name for the type form string e Functional form of short range potential 106 id int Internal ID of the atom type within its parent forcefield name string Name of the type neta string The original type description used to identify the type nparams int The number of parameters used by the functional form of the interaction ff forcefield Parent forcefield conta
114. atisfactory way e g that employed in Vega ref XXX Aten uses the latter style and provides a clear powerful and chemically intuitive way of describing atom types in most importantly a readable and easily comprehended style Type descriptions are used primarily for assigning forcefield types but also make for an extremely useful way to select specific atoms as well 12 5 1 Language Examples Type descriptions in Aten use connectivity to other atoms as a basis extending easily to rings and the constituent atoms lists of allowable elements in certain connections atom hybridicities and local atom geometries Descriptions can be nested to arbitrary depth since the algorithm is recursive and may be re used in other atom s type descriptions to simplify their identification Time to jump straight in with some examples Note that these examples only serve to illustrate the concepts of describing chemical environment at different levels They may not provide the most elegant descriptions to the problem at hand don t take advantage of reusing types see Section 12 5 4 and certainly aren t the only ways of writing the descriptions Example 1 Water ee H H Consider a water molecule If you were describing it in terms of its structure to someone who understands the concept of atoms and bonds but has no idea what the water molecule looks like you might say A water molecule contains an oxygen that is connected two hydrogen atoms by
115. atom if any 0 position 1 force 2 velocity colour double 4 RGBA colour of the vertex components ranging from 0 0 1 0 vector vector Vertex coordinates 8 2 29 Grid Type The grid type stores all information for a single grid structure associated to a model Table 8 18 Grid Type Members Member Type RW Description axes unitcell Axes system for the grid stored in a unit cell structure colour double 4 The primary colour of the grid data cutoff double The lower primary cutoff value name string Name associated to the grid data nx int Size of grid data in the x dimension ny int Size of grid data in the y dimension nz int Size of grid data in the z dimension origin vector Coordinates of the origin lower left hand corner of the grid data outlinevolume int Flag specifying whether a bounding volume cuboid should be drawn for the grid periodic int Flag specifying whether the grid is periodic e g 112 at the edges data from opposite side should be used to form grid secondarycolour double 4 The secondary colour of the grid data secondarycutoff double The lower secondary cutoff value secondaryuppercutoff double The upper secondary cutoff value shiftx int Shift value in points for the grid along its x axis shifty int Shift value in points for the grid along its y axis shiftz int Shift value in points for the grid along its z axis uppercutoff double The u
116. atom and all that occur after 1t 230 deselectf Syntax int deselectf string format Deselect atoms using the same syntax as the deselect command but constructing the string using a C style printf approach Useful when two integer numbers defining a range of atoms to deselect are stored in two local variables for instance or when the selection range must change dynamically in a loop For example int i 10 Claseulkacicis Weisel ON deselects atom ids 10 to 20 inclusive deselectfor Syntax int deselectfor string code Compiles and executes the code supplied within a loop which runs over all atoms The control variable of the loop in which the code is inserted is of type atom and is named i The code provided should use this pointer to decide whether or not the atom in question should be selected or not returning TRUE or FALSE in the process A return path resulting in FALSE need not be specified since this is the default if the code supplied does not return a value For example deselectfor if i z 6 return TRUE will deselect all carbon atoms in the current model deselecttype Syntax int deselecttype string int element el string neta Deselect all atoms in the current model matching the element and NETA type description specified For example deselecttype H O C 231 will deselect all hydrogen atoms bound to oxygen atoms which are i
117. atom ii in aten model selection Panta Arton Iises ele creo ae 166 This will select all hydrogen atoms in the current model then loop over the atom selection twice once with a for loop and once with a for in loop both of which are equivalent if Syntax if condition commands else if commands else commands The if statement permits sections of code to be executed based on the assessment of logical comparison of values If the supplied condition evaluates to be TRUE then the following commands are executed otherwise nothing happens In the second form of the command if the condition evaluates to be false then the second set of commands are executed instead If multiple commands are to be executed then they should be enclosed in curly brackets as written in the syntax above If only a single command is to be executed the curly brackets may be omitted Typically comparisons are made between two variables for example aie weal S wee checks for var1 being greater in value than var2 executing the following commands if this turns out to be true The comparison operator may be any one of the following symbols Table 9 1 Comparison Operators Operator Meaning as Equal to Not equal to lt gt Not equal to gt Greater than lt Less than gt Greater than or equal to a Less than or equal to In truth the condition part may be any expression command or amalgam of both provi
118. aults are used if this is not provided For example mopacminimise minimises the current model with the default options listed above mopacminimise UHF TRIPLET PM6 DH2 minimises the current model assuming a triplet state with the UHF method and the PM6 DH2 hamiltonian sdminimise Syntax void sdminimise int maxsteps 206 Optimises the current model using the Steepest Descent method For example sdminimise 100 minimises the current model for a maximum of 100 steps with a simple steepest descent minimiser 9 21 Model Extras Commands Store and manipulate molecular orbital data vibrations and z matrix elements newbasisshell Syntax basisshell newbasisshell atom int id string type Adds a new basis shell definition to the current model returning the generated structure The atomic centre on which the basis function exists must be provided either as an integer or an atom pointer from which the integer ID is extracter The type of the basis shell should correspond to one listed in basis shell types For example basisshell newbasisshell 15 D creates a new D orbital shell centred on atom 15 neweigenvector Syntax eigenvector neweigenvector int size auto Adds a new empty eigenvector to the current model If the size argument is given the eigenvector array will contain this many elements Otherwise the size of the array is determined by the total n
119. ay Syntax 222 int readdoublearray double d int n Read n consecutive integer values whose individual size is determined from the result of calling sizeof double from an unformatted binary input file placing in the array d provided The size of the array provided must be at least n The command returns a Read Success integer For example double data 45 int success readdoublearray data 45 reads 45 double numbers into the array data readint Syntax int readint int readint int nbytes Read an integer value the size determined from the result of calling sizeof int from an unformatted binary input file Alternatively if a valid number of bytes is specified and corresponds to the size of another class of int e g long int on the machine this size is used instead For example int i readint reads an integer number into the variable i readintarray Syntax int readintarray int il int n Read n consecutive integer values whose individual size is determined from the result of calling sizeof int from an unformatted binary input file placing in the array i provided The size of the array provided must be at least n The command returns a Read Success integer For example int data 100 int success readintarray data 100 reads 100 integer numbers into the array data 223 readline Syntax int readline int double string var
120. batch switch this mode runs all commands provided on all models once the last model has been loaded The models are then saved in their original format to the same filename Note that if the an export filter does not exist for the original model file format changes to that model will not be saved It is advisable to work on a copy of the model files when using this command or to use batch export mode to save to a different format in order to preserve the original files The GUI is not automatically started in batch mode For example to transmute all iron atoms into cobalt for a series of xyz files named complex 001 xyz complex 002 xyz etc bob pe gt aten batch c select Fe transmute Co complex xyz Export Mode Invoked by the export switch in export mode each model file specified on the command line is loaded and immediately saved in the format specified by the provided nickname allowing multiple files to be converted to a different format at once The GUI is not automatically started in export mode For instance to convert three DL_POLY CONFIG files and an xyz into mol2 format bob pec gt aten export mol2 biol CONFIG bio2 CONFIG watercell CONFIG random xyz 32 If specified in conjunction with the batch switch batch export mode is entered instead and any supplied commands are executed on each loaded model file before it is saved The original model files are not modified Batch Export Mode In
121. bl bz doubl centrex doubl 00000000000 Length of cell axis A Angle between cell axes B and C Length of cell axis B Angle between cell axes B and C e Length of cell axis C x component of cell axis A y component of cell axis A z component of cell axis A x component of cell axis B y component of cell axis B e z component of cell axis B x coordinate at centre of defined cell 128 centrey double y coordinate at centre of defined cell centrez double z coordinate at centre of defined cell cx double x component of cell axis C cy double y component of cell axis C CZ double z component of cell axis C density double Density of the current cell gamma double Angle between cell axes A and B matrix double 9 Cell axis matrix containing all three cell vectors For example ax matrix 1 ay matrix 2 etc sgid int Integer ID of the current spacegroup sgname string Symbol of the current spacegroup type string Type of the current unit cell see Cell Types in Section 16 4 volume double Volume of the cell in cubic 8 2 38 UnitCell Type Functions mim Syntax vector mim atom i atom j Returns a vector containing the minimum image coordinates of the atom i with respect to the reference atom j Note that the coordinates of both i and j are not modified in any way mimd Syntax vector mimd atom i atom j Returns the minimum image vector between the
122. can be fixed as follows Since keymaps are not used the offending lines can be commented out in readline h Locate the file by default it is installed in C Program Files GnuWin32 include readline readline h and edit it with Notepad or something similar Put a comment marker at the very beginning of line 356 and a comment end marker at the very end of line 364 Rerun nmake and everything should be fine 2 3 11 Anything Else Instead of downloading the zipped source of Aten you could download a Windows subversion client and maintain an up to date copy of the source on your machine useful if you want to frequently get the latest updates There are many subversion clients available but Win32svn http sourceforge net projects win32svn works well for me 11 3 Frequently Encountered Problems What follows is a sort of mini FAQ detailing some commonly encountered problems and issues when compiling and executing Aten for the first time and also some of the more persistent problems that various platforms exhibit 3 1 Configuration Errors ALL autogen sh line 35 libtoolize command not found You need to install the 1ibtool package it should be on the original CD of your linux distro or on one of the billions of repository mirrors around the world OSX Error Possibly undefined macro AC_DEFINE When running autogen sh autoconf sometimes fails with configure ac 16 error possibly undefined macro AC DEFIN
123. cefield description of your system in the format that you require it with a different filter Please don t use Aten as a literal black box though and blindly write out forcefield files without checking them While it will certainly make the process of generating your forcefield descriptions easier the art of determining the correct types in the first place and hence the correct forcefield terms is not definite for larger forcefields that cover many atom types Check the output a cursory glance of the selected forcefield types is an excellent idea and a good habit to get in to Aten is in continual development so if you get stuck find a bug or have a suggestion to make please go to the Support page of the website and visit the forums or send an email directly Making Aten better depends to some degree on user feedback 1 2 Feature Matrix TODO 1 3 Supported File Formats A list of formats currently supported by Aten follows as well as the file extensions and assigned filter IDs Remember adding support for other codes and formats is in your hands with Aten s filters see Section 11 Format Aten Keyword Format Cambridge Structural Database Service Crystallographic Information File DL_POLY Configuration EPSR ATO File GAMESS US Output Log GAMESS US Input File Gaussian Input File Gromacs Configuration Mopac Archive File Mopac Control File MDL Molfile MSI Cerius2 Model File Protein Databank PDB
124. ces are given as two sets of nine numbers that define the vectors of the axes When supplying atom IDs the x axis is taken to be absolute the y axis is orthogonalised w r t the x axis and the z axis is taken as the cross product between the x and y axes Note that providing the definition of the z axis is still important however since the vector cross product is adjusted if necessary to point along the same direction as this supplied z axis When supplying the complete matrices no orthogonalisation or normalisation of the axes is performed permitting arbitrary scale and shear operations 253 For example MARCO SS ik Wy tO Wil 12 as iM 15 5 defines a the current selection s frame of reference as in terms of atom IDs X 1 gt 2 Y 1 gt 3 and Z 1 gt 4 which will be rotated such that it corresponds to the new frame of reference again defined by atom IDs X 10 gt 11 Y 12 gt 13 and Z 14 gt 15 MENE OS EN O SS 0 192 0007187 DATO USO Ono5534 O 460G A TAT D gt Arg Lo 0D Oj Lp 0 Oy Oj 41 defines a the current selection s frame of reference as the vectors X 0 7348 0 0192 0 678 Y 0 4979 0 6635 0 5584 and Z 0 4606 0 7479 0 47801 which will be rotated into the standard reference frame matrixtransform Syntax void matrixtransform double ax double ay double az double bx double by double bz double cx double cy double cz void matrixtrans
125. cho Setting Visual Studio environment SVCSTUDIO C Program Files Microsoft Visual Studio 10 0 SWINSDK C Program Files Microsoft SDKs Windows v7 1 System variables Senv VSINSTALLDIR VCSTUDIO Senv VCINSTALLDIR S VCSTUDIO VC Senv FrameworkDir C Windows Microsoft NET Framework Senv FrameworkVersion v2 0 50727 Senv FrameworkSDKDir S VCSTUDIO SDK v3 5 Senv DevEnvDir SVCSTUDIO Common7 IDE Executable path Senv PATH VCSTUDIO Common7 IDE Senv PATH SVCSTUDIO VC BIN Senv PATH S VCSTUDIO Common7 Tools Senv PATH SVCSTUDIO Common7 Tools bin Senv PATH SVCSTUDIO VC PlatformSDK bin Senv PATH SVCSTUDIO SDK v2 0 bin Senv PATH SVCSTUDIO VC VCPackages Senv PATH SWINSDK Bin Include directories Senv INCLUDE VCSTUDIO VC ATLMFC INCLUDE Senv INCLUDE SVCSTUDIOAVCA INCLUDE Senv INCLUDE SVCSTUDIO VC PlatformSDK include Senv INCLUDE VCSTUDIO SDK v2 0 include Senv INCLUDE SWINSDK Include Libraries Senv Senv Senv Senv Senv Senv else echo Set Senv sie LIB S VCSTUDIO VC ATLMFC LIB LIB SVCSTUDIO VC LIB LIB SVCSTUDIO VC PlatformSDK lib ONES RUDRON S DENY ZONTA LIB SWINSDK Lib LIBPATH SVCSTUDIO VC ATLMFC LIB No Visual Studio installed or incorrect version string used up Qt environment variables ODDTR SG Ore NZOTO US test path
126. ck in the forcefield file When calling the functions Aten provides the necessary structure in which the generated parameters should be stores In the case of the VDW generating function the actual atomtype structure which is missing the data is passed see the f fatom variable type In the case of intramolecular interactions Aten creates and passes a new empty ffbound container in which the functional form of the interaction and the relevant data values should be set A number of f fatom references are also provided corresponding to the atom types involved in the bound interaction and from which the necessary data values may be retrieved using the relevant data accessors For bound interactions it is not necessary to set the equivalent names of the involved atom types since this is done automatically The recognised function names and their arguments are as follows anglegenerator Syntax int anglegenerator ffbound newdata atom i atom j atom k Called whenever function data for an unrecognised angle between the atom types currently assigned to atoms i j and k is needed Generated parameters should be store in the passed newdata Structure bondgenerator Syntax 302 int bondgenerator ffbound newdata atom i atom j Called whenever function data for an unrecognised bond between the atom types currently assigned to atoms i and 7 is needed Generated parameters should be store in the passed newdata Structure
127. ck the version If its version 3 x x then you will need to reconfigure the build as follows Each of the three Qt4 utilities needed to compile Aten moc rec and uic can be specified explicitly with three configure options with qtmoc with qtuic and with qtrcc Typically the Qt3 binaries are located in usr lib qt3 bin while the Qt4 binaries are in 12 usr bin but this may not be the case on your particular system For the sake of argument let s say they are then the configure command will be run as follows bob pe src aten gt configure with qtmoc usr bin moc with qtuic usr bin uic with gtrcc usr bin rcc ALL Error This file was generated using the moc from 3 X X It cannot be used with the include files from this version Again this is usually related to both Qt3 and Qt4 development tools being installed simultaneously See the previous question and its solution above OSX Undefined reference to ___ stdoutp expected to be defined in usr lib libSystem B dylib Chances are you have an older operating system Panther 10 3 9 is confirmed to show this error Since the Universal Mac binaries are built on a machine with Snow Leopard 10 6 this error can only be avoided by upgrading your operating system or compiling Aten by hand 3 3 Usage Errors LINUX I saved an image from the GUI and it was completely black corrupt Why A common issue with integrated Intel graphics chips but may a
128. clusions For a full list see the reference page at cplusplus com or cppreference com The list of printf features that are not currently supported in Aten are as follows e The pointer specifier p is not supported To print out reference addresses use 14 e The single character specifier 3c is not supported e Output of long doubles by prefixing a specifier with L e g SLe is not supported 11 3 5 Extra Specifiers Within Aten As well as the mostly complete standard set of specifiers provided by C Aten also includes some other useful specifiers that may be used in formatted input and output Table 11 6 Extra read write specifiers Specifier Meaning Relevant to formatted input only Discard the next item regardless of its type A 285 corresponding variable argument need not be provided Read characters starting from the next delimited argument until the end of the input line is encountered i e rest of line specifier A corresponding string variable should be provided oO R 11 3 6 Escaped Characters Table 11 7 Escaped characters in format strings n Print newline next character will appear on the next line Nr Carriage return vt Tab character 11 3 7 Delimited Reading and Writing Formatting strings or format specifiers can be used to specify the layout of data items on a line when reading or writing data but if the data are separated by whitespace characters such as spaces or tabs or alternativel
129. cule and bears a lot of connections and provide an unambiguous type description 309 12 6 NETA Reference This section lists all the available commands that may make up a type description Many keywords only make sense within the bracketed parts of keywords that expand the depth of the description For instance it is meaningless to specify the connection type with the bond keyword in the root of a typing command since no connections are relevant at this point X any bond to X X specifies that a connection to X must exist but makes no demand of the type bond order of the connection X may be an element symbol an id for another type specifier or a list in square brackets containing one or both of these to allow more flexible specifications Specifying an unknown connection with x is often useful in for example aromatic rings or conjugated systems where the connection might be either a double or single bond Table 12 2 NETA X Keyword Examples Command Meaning aC Any bond to a carbon atom amp 101 Any bond to an atom which matches type ID 101 see Reusing Types in section 12 5 4 N S P Any connection to either nitrogen sulfur or phosphorous yO Explicitly states that there should not be a bond to an oxygen atom X single bond to X X specifies that a single bond to X must exist X may be either an element symbol an id for another type specifier or a list containing one or both of these to allow more f
130. d or carboxylic acid adjacent to a carboxylic acid adjacent to alcohol For both we only need describe the first neighbours of the atoms For the first 3 Cia E nbonds 4 H H C Methylene Carbon 4 Gos nbonds 3 0 bond double 0 C Carboxylic Acid C Note the ordering of the oxygen connections for the carboxylic acid carbon where the most qualified carbon is listed first This is to stop the doubly bound oxygen being used to match O subsequently preventing a successful match This is a general lesson bound atoms with the most descriptive terms should appear at the beginning of the type description as it is read left to right and those with the least left until the end Where all three carbons need to be identified separately we may write 5 SOLO nbonds 4 H H C 0 CH2 adjacent to OH 6 C COOH e nbonds 4 H H C C CH2 adjacent to COOH 7 Oc E nbonds 3 0 bond double 0 C Carboxylic Acid C Let us now assume that the hydrogens within the alcohol and carboxylic acid groups must also be seen as different types In this case the second neighbours of the atoms must be considered 8 HO H VOS R 1310 740 Alcoholic H 9 Bi lops H C 0 bond double Carboxylic acid H The assignment is thus based entirely on the nature of the carbon atom to which the OH group is bound since this is the next available source of connectivity information The determination of the three different oxygen at
131. d by its absolute position in the system and commonly belongs to one other cuboid determined by adding half of the cuboids dimensions on to the atoms position While a little counterintuitive potentially adding atoms to a neighbouring cuboid along this diagonal vector allows the final calculation of distances between pairs of atoms to consider only eight neighbouring more correctly overlapping subvolumes rather than the 26 needed if each atom belongs exclusively to only one cuboid For atoms that exist in subvolumes along the edges of the whole volume these are also added to the subvolume s on the opposite side s to account for minimum image effects in periodic systems Once the effort has been made to assign atoms to cuboids the final loops to calculate distances runs over a much reduced subset of atom pairs owing to the partitioning A loop over cuboids is performed first considering all atom pairs within the same cuboid and then extending this to consider distances between a particular atom of this central cuboid and its eight overlapping neighbours There is some redundancy of atom pairs since the same pair may be considered twice when taking into account the overlapping cuboids However in the interests of facile book keeping this is not checked for explicitly during the running of the algorithm 1 Covalent radii revisited B Cordero V G mez A E Platero Prats M Rev s J Echeverr a E Cremades F Barrag n
132. d it into the GUT you can do the following aten data test cellulose cif c savebitmap png cellulose png quit Doing this will load the cellulose model save an image of it and then quit without ever starting the GUI By default the size of a saved image is 800x600 but optional arguments to the savebi tmap command allow this to be set explicitly 40 5 9 Calculating a Torsion Energy Profile CLI This example demonstrates a simple energy analysis procedure in which we load a model and perform a scan of a geometric parameter calculating the energy at each step The methanol model and OPLS AA forcefield both supplied with Aten are used by the command but of course can easily be substituted with your own choices The command first sets the electrostatic calculation method to be the simple Coulomb sum since the methanol model is non periodic and prior to the loop starting a text header is written The loop iterates a variable phi over the range 180 to 180 degrees in steps of 5 and is used to set the torsion angle between atoms 2 1 4 and 6 corresponding to one of the H C O H torsions in the model A line of output is written for each torsion angle considered providing the total torsion van der Waals and electrostatic energy of the system at this geometry aten ff oplsaa ff data test methanol inp q c aten prefs elecmethod coulomb printf Torsion Angle E Torsion E VDW E Coulomb n f
133. d once you are confident that the forcefield types are consistently correct Larger forcefields e g OPLS AA by Jorgensen et al do not have a complete set of type descriptions implemented in Aten Once more if your add some in please send them to me so they can be included in a future revision of the code tris projectaten net Acknowledgements Aten is maintained entirely by T Youngs However many people have contributed useful thoughts ideas bugfixes and motivation to the project over its lifetime These people are in no particular order A K Croft and crew Mac afficionado supreme fault finders S Cromie algebraic guidance A Elena bug finder extraordinaire pathological case locator Windows Mac building and packaging D Pashov Windows Mac building and packaging S Norman icon judgment N C Forero Martinez and M Smyth bug finding bug finding and bug finding Table of Contents 12 A O 1 IT A elude epee an dha teed NE eld tea a seve adel tea EELEE ESE TE en 1 1 2 Feature Matricula alada 1 1 3 Supported File Ports ta 1 2 Installation pipi ada 3 2 1 From Precompiled Packages All Platforms onoocnnncnnccnnonnnocononnnoncconancnnncnononnncninn no 3 2 2 From Source Linux Mac OS X pramena n n a A E A GROR 3 23 From S r e WINS dali a iai 6 3 Frequently Encountered Prol i a ane eae 12 Sale SCombiguration ELOTE 12 Se COMP ALON o ae le 12 Oye Usage Errors ene a a a
134. d one in but its marginally more interesting to build one from scratch So we ll place an oxygen atom down somewhere and automatically add hydrogens to it Main Toolbar Create a new empty model if you don t have one already with Y Build In the Build Window change the active element to oxygen on the Edit page by clicking E Select the draw single atoms tool and click once somewhere in the empty model to draw an oxygen atom Add hydrogens to the model by clicking AddH Model A Aten vL7 r1671 Unnamed002 lt lt no filename gt gt Modified y Ye File Edit View Selection Model Trajectory Forcefield Settings Scripts Help JPABA DY DA tHe e seatLanee r Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click drag 3 Atoms 18 015000 g mol or rotate in local frame right click drag ctrl remove from selection Non periodic Run the Disorder Builder The Disordered Builder adds molecules into a new or existing model with a unit cell The only requirement of the Disorder Builder is that all the models you wish to add must be loaded into Aten before the builder is run Everything else is handled by a wizard which guides you through the process 18 T Disorder Run the Disorder Builder wizard Disorder Wizard Y UD Step 1 5 Model Target Select the target model for the build or choose to create a new one Use Existing M
135. dary 190 gridlooporder 190 gridorigin 191 gridortho 191 gridstyle 191 gridusez 192 gridvisible 192 gui 247 help 247 hide 132 if 167 info 210 initgrid 192 interdef 175 invert 232 itoa 243 label 196 lastframe 250 lastmodel 211 linetol 205 listcomponents 158 listmeasurements 200 listmodels 211 listpatterns 218 listscales 155 listscripts 229 listsites 239 In 197 loadff 175 loadgrid 193 loadmodel 212 loadscript 229 loadtrajectory 250 locate 143 log 197 lowercase 243 map 175 matrixconvert 253 matrixtransform 254 mcaccept 215 mcallow 215 mcmaxstep 215 meminimise 206 336 mentrials 216 measure 201 measureselected 201 millercut 149 mirror 257 modelenergy 162 modelforces 180 modeltemplate 212 mopacminimise 206 move 143 movetoend 143 movetostart 143 newatom 144 newatomfrac 144 newbasisshell 207 newbond 138 newbondid 139 neweigenvector 207 newff 176 newglyph 185 newerid 193 newmodel 212 newpattern 218 newsite 239 newvibration 208 nextarg 221 nextframe 250 nextmodel 213 nint 198 normalise 198 null 247 orthographic 258 pack 150 parentmodel 213 paste 159 peekchar 221 peekchari 221 perspective 258 prevframe 250 prevmodel 213 printcell 150 printelec 162 printenergy 163 printewald 162 printf 203 printforces 180 printinter 162 printintra 163 printmc 216 printsetup 176 printsummary 163
136. ded the end result of executing it is a single value The type of the final result doesn t even matter since conversion to a boolean is guaranteed Deep down in the logic of Aten integers are at the heart of it all with zero or any negative number being FALSE and any positive number meaning TRUE For example so e sk 107 ase 1 9 jaa Moore a 167 in this case Hooray will be printed because i is greater than 5 int i 10 j 20 te 1 3 primer Vooral Wa a but in this case Hooray will not be printed because i is not greater than j ate a 10 3 O alse 12 9 Jaca Mora clse if ronime Valo Sme Wo 9 ak sje Here the test fails for the same reason but since an else part was provided we still execute some commands printing Too small and setting the variable i equal to 3 Since any positive number is TRUE we can simply test the value of a variable be Gt SOS sige 5 aa SOON NAAN E atom a newatom H if a printf New atom n In a similar way a reference variable has a positive integer value at its heart and so can also be tested in this way atom a newatom H double alpha 100 0 if a amp amp alpha lt 50 0 printf Alpha and atom are OK n else printf No good n Two or more consecutive conditions can be tested in order to determine truth in this case using the and operator amp amp Here the value of the reference variabl
137. des on startup nolists Prevent the use of OpenGL display lists for rendering Simple vertex arrays will be used instead Try this option out if rendering is corrupt or Aten crashed unexpectedly on startup The rendering will be slower but more compatible nopack Prevent generation of symmetry equivalent atoms from spacegroup information in loaded models overriding any occurrences of the pack command is used in the corresponding filter nopartitions Prevents loading of partitions on startup noqtsettings Don t read in any system stored Qt settings on startup such as window positions toolbar visibilities etc using the defaults instead 50 P pack Force generation of symmetry equivalent atoms from spacegroup information in loaded models even if the pack command was not used in the corresponding filter pipe Read and execute commands from piped input on startup process Enter process mode where commands are run on models but no changes are saved instead the GUI is started once all commands have been executed See Section 6 3 for details and a list of other modes Q q quiet Prevents nearly all text output from Aten including error messages and the like but does allow printing of user output via the printf command in scripts and commands passed with command Useful in order to print clean data to a file or standard output S s lt file gt script lt file gt Specifi
138. ditbox and will be executed immediately This command will then be added to the list above and can be single clicked to return it to the editbox for tweaking or re editing or double clicked to execute it again The list of stored commands is saved when Aten exits and loaded back in when restarted 67 Command Console o x Prompt Interactive Scripts Command Help Variables Variable Type 1 aten aten amp 0x9 lt c lt gt CA Force Update Figure 7 14 Command Window Interactive page For when single line commands are too inflexible the interactive page mimics a more proper console like environment Here variables can be defined in one instance and referred back to and manipulated in others much like a normal shell A list of variables currently defined in the local scope is shown in the uppermost part of the window Command Console o x Prompt Interactive Scripts Command Help Load ReloadAll Run Selected Figure 7 15 Command Window Scripts page Scripts can be loaded in from here and executed at will by double clicking individual scripts in the list or selecting multiple scripts and clicking the Run Selected button Any script files loaded in this way are remembered when Aten exits and are loaded back in when restarted All scripts can be reloaded from disk if for example changes have been made to one or more files after they were loaded in by clicking the Reload All button 68 Command Consol
139. double 0 529177249 AVOGADRO double 6 0221415E23 DEGRAD double 57 295779578552 FALSE int 0 NULL int 0 PI double 3 14159265358979323846 TRUE int 1 In addition all element symbols found in the input will be seen as their equivalent integer atomic number So instead of having to provide short strings containing the element name to for example the transmute command simply the capitalised element name itself may be used Thus 103 transmute Xe y T transmute X 5 e transmute 54 are all entirely equivalent 8 1 5 Blocks Scope and Variable Hiding As with C variable scope is employed in Aten meaning that a variable may be local to certain parts of the code filter script In addition two or more variables of the same name but possibly different types may peacefully co exist in different scopes within the same code filter script Consider this example int n 4 i 99 rta WS Vin a if n 4 96 Tigi SL OA reia ade EA ac Wal Vin 1 9 Will generate the following output 99 99 Why Well even though two variables called i have legitimately been declared the second declaration is made within a different block enclosed within a pair of curly braces Each time a new block is opened it has access to all of the variables visible within the preceeding scope but these existing variable names may be re used within the new block in new declarations and does not affect t
140. e GUI all filters are available in the file dialogs 11 1 4 Filter Definitions Filter definitions are made in a filter file in a similar way to declaring a user subroutine or function see Section 8 1 7 The filter keyword marks the start of a filter definition and contains a list of properties in parentheses that define the subsequent filter its name and how to recognise the files from their filenames and or contents that it is designed for The definition of the filter to import XYZ style model data is as follows filter type importmodel name XMol XYZ Coordinates nickname xyz extension xyz glob xyz id 3 commands The comma separated list of properties defines the type of filter type importmodel and how to recognise files of that type e g extension xyz amongst other things 268 The full list of possible properties is as follows Table 11 1 Filter Definition Keyword Summary exact Comma separated list of filenames that are of this type extension Comma separated list of filename extensions that indicate files of this type glob Shell style glob to use in file fialogs in order to filter out files of the described type id Numerical ID of the filter to enable partnering of import export filters for files of the same type name Descriptive name for the filter shown in file dialogs etc nickname Short name used by commands in order to identify specific filters search Provides a string to se
141. e a and the value of alpha are both checked and the text Alpha and atom are OK is only printed if both turn out to be TRUE if time 0 printf There is no time else if time gt 5 printf There is more than enough time else printf There is only a little time Multiple if tests can also be nested to create a sequence of tests As soon as a condition is encountered that equates to true the accompanying commands are executed and any subsequent else d tests or commands are ignored return Syntax return 168 return value Used in user defined functions and returns control immediately back to the calling function In the case of a void function no return value must be specified Similarly for functions returning a value a valid value of that type must be given while Syntax while condition commands The while loop is another cousin of the for loop and as with the do while loop there is no control variable The termination of the loop depends on the condition which is tested at the beginning of the loop before execution of the commands If TRUE the commands are executed but if FALSE the loop ends without executing the commands and meaning that it is possible that the commands are never executed For example int i 1024 male ab gt 100 sk 3 Y 29 jorcslioncsr Vs Fecha alla will print out the following 512 ES N al Oy H H H H IEA D
142. e desired element A reference to the new atom is returned For example atom i newatom N places a nitrogen atom at the current pen coordinates atom i newatom 18 5 2 0 0 places an argon atom at the coordinates 5 2 0 0 0 0 newatomfrac Syntax void newatomfrac int string el double double y double z void newatomfrac int string el double double y double z double vx double vy double vz void newatomfrac int string el double double y double z double vx double vy double vz double fx double fy double fz 144 Create a new atom of element e1 at the specified fractional coordinates velocities and forces are optional Either the integer atomic number or the symbol name of the element may be used to identify the desired element A reference to the new atom is returned For example Boom to NEVA Comi rac MC O45 OS Oo Sie places a carbon atom at the centre of the model s cell reorder Syntax void reorder Adjust the ordering of atoms in the current selection such that atoms in bound fragments molecules have successive IDs Useful to recover molecularity in order to apply a suitable pattern description to the system For example reorder rotx Syntax void rotx double angle Rotates the reference coordinate system about the x axis by angle degrees For example OSO ON 4 rotates around the x axis by 90 degrees r
143. e dld 3 be cake aac As a eacel 267 A MERA COLO A E E T E EE E 279 11 3 Reading and WINE id aid 283 12 For efields and Typing siii er a oea EEA EE Genes 289 TZT ONCE eiii 289 12 2 Supplied Forces iii de 290 12 3 Rey word Reference tii 293 12 4 Rule Based Forcefields mcme ii i h 302 12 5 Typi onetiese a EES be ioe NEE NE EEE ATE E N TR RES 304 12 6 NETA Reference nuncio din 310 13s A la roe e un Gebsedeaeugs hae euon doe T aaeutuanhe 316 13h VW Punctional Forms sisse ernn Rhode ees ee Be 316 182 Bond Eunice etal aaiane 317 O a A Giana as aah sea ae eee ai 318 13 4 orion Functional PO Oo 319 14 External PORTS at deine A ees ed ee A AA A eee 320 T41 Movie Genero e ne ae dee 320 142 MOPA Cardoso 320 1S5 Metodo seed e Mare ve deol o de 321 15 1 Custom Alo ad 321 15 2 Literature Methods AA ih ies gh ad see Sk wae a A he tance ot 325 16 MURS PAIOIS 554 6 sto he testa ti e ot et 326 16 Basi MAS alba 326 A 10 ato G DAA oe AE E E EE AEE A E E tes oopneduae ness 326 as Bound Os 326 AE A SE INT Se fe a N a ole SC 327 16 3 Colqur SCC Sianna n a E E E E Soca tala cea eevee cy 327 166 Combination Rules 0 da 327 16 7 Drawing Styles ini id aia 328 16 8 Ennery US ui ir ds 328 160 Glyph TP 328 AI ON 329 16 1 Grid Types iia 329 16 12 16 13 16 14 16 15 16 16 TABS HW Sse sais evade taeda ve cls Seatac se pene ee de ne ee 329 Output TV Pe mirra a iii 330 Parse Opus sia sisicasvsnseanti
144. e following examples Table 10 2 Pattern Examples System Atom Ordering Automatic Pattern 264 H1 02 H3 HOH 3 H4 O5 H6 H7 08 H9 HL C12 HC1 1 HOH 2 H3 04 H5 H6 O7 H8 H1 02 H3 HOH 1 HC1 1 HOH 1 H4 C15 H6 O7 H8 H1 02 H3 HOH 1 H 1 HHO 1 C1 1 H4 H5 06 H7 C18 In 1 the three water molecules are identical with respect to the ordering of the atoms so our description consists of a single pattern describing one HOH moiety Obvious huh The two component system illustrated in 2 has all molecules of the same type one after the other giving a simple two term pattern However in 3 the two water molecules are separated in terms of their order by the HCl and so a three term pattern results In 4 there are from the point of view of the program three distinct molecules since the ordering of atoms in the two water molecules is different and so three terms are again necessary in the pattern description There are likely to be many possible pattern descriptions for systems some of which may be useful to employ and some of which may not be Take the well ordered system 1 four different ways to describe the system are HOH 3 HOH 1 HOH 1 HOH 1 265 HOH 2 HOH 1 HOH 1 HOH 2 All are equivalent and will give the same energies forces Sometimes it is useful to treat individual molecules as separate patterns in their own right since it allows for calculation of interaction energie
145. e forcefield selected in the list is the current forcefield and the one used by all other actions on the page Forcefields are loaded unloaded and edited with the buttons immediately underneath the list The Associate panel links the selected forcefield to one or more models and their patterns the Current Model button links the current forcefield to the current model while the All Models button links the current forcefield to all loaded models The Pattern in Current Model 73 button brings up a dialog listing the patterns of the current model from which one is selected to link the forcefield to A forcefield associated to an individual pattern will be used in preference to the forcefield associated with its parent model and if none is assigned the default forcefield Automatic atom typing can also be performed or removed from here Finally you may check that a full expression is available for the current model by pressing the Create button in the Expression panel at the very bottom The nearby checkbox determines whether atomic charges should be assigned from atom type information or whether the current charges if any should be left intact Energy Forcefields o x Energy Forcefields Manual Typing UFF v WW Open X Close Edit 0 Save As Associate Current Model All Models Pattern in Current Model Automatic Typing Apply Jl Remove Expression Create Y Assign FF Charges Figure 7 18 Forcefi
146. e installation location is set to by default it is C Program Files Microsoft Visual Studio 10 0 because you ll need this later on for the installation of Windows PowerShell Chances are you 1l need to restart your machine after the installation 2 3 2 Install the Windows SDK Get the Windows SDK from http msdn microsoft com en us windows bb980924 or search for Windows SDK on the internet Note that the download is described as being for Windows 7 and NET but this is fine since it s backwardly compatible with XP Run the installer winsdk_ web exe and accept the license and again take note of the installation directories since they need to be provided in the PowerShell setup later on The default installation options are fine although you can uncheck the installation of Samples since they are not required Once installation has finished the Windows Help Centre may pop up and ask where your local resources are This can safely be canceled 2 3 3 Install CMake Download the lastest CMake installer from http www cmake org version 2 8 4 at the time or writing and install it Make sure you choose to add CMake to the PATH for all users when running the installation 2 3 4 Install Readline Go to http gnuwin32 sourceforge net packages readline htm or search for Windows Readline on the internet and download the Complete package except sources installer around 2 3 Mb If you choose to i
147. e o x Prompt Interactive Scripts Command Help Search colouratoms currentatom GE gt gt lt Figure 7 16 Command Window Command Help page All of Aten s commands are listed in the panel in the upper half of the page while the syntax and description of any command selected in the list is displayed in the lower half The list can be searched by typing in a partial name in the Search box at the top 69 7 11 Disorder Builder Wizard TODO Disordered Builder Wizard The Disorder builder wizard generates a disordered system involving a collection of molecules This can be a snapshot of a liquid suitable for use in a molecular dynamics program a mixture of two or more species an interface between two or more species or something more exotic The disordered builder requires that all molecules which are to be included in the system are currently loaded and none must have its own cell defined However while all models which are to be inserted into the final system may not possess a unit cell a periodic model can be the target of the insertion and may contain an existing collection of molecules atoms In order to begin the disordered wizard click on the Disorder icon in the Edit section of the tool box This will present the first of five steps designed to build your system In the first wizard screen the model target may be assigned If a cell has already been defined choose the first choice Use
148. e present in an aromatic environment e g in an aromatic ring or that a ring should itself be aromatic Table 12 10 NETA aromatic Keyword Examples Command Meaning N aromatic Specifies a nitrogen connected by any bond which is present in an aromatic environment C ring aromatic Single bond to a carbon atom which is in an aromatic ring noring noring indicates that the atom must not be present in any rings Table 12 11 NETA noring Keyword Examples Command Meaning O noring Single bond to an oxygen which is not present in a ring planar The planar keyword specifies that the atom target should be planar which is to say no bond from the atom may be more than 15 out of the plane formed by the first two bonds to the atom Table 12 12 NETA planar Keyword Examples C planar Single bond to a carbon atom which is roughly planar ring ring denotes that the target atom if specified in the root of the description or a bound atom if used inside the associated bracketed part should be present in a ring structure of some kind The ring keyword alone simply demands that the atom is present inside a ring of some size but may take an optional bracketed part describing more fully the number of atoms in the ring and the individual nature of each of these atoms Within the bracketed part bound atoms may be specified as usual in the contained neta but the connection type is irrelevant as it is only the pr
149. e specified colourscale For example clearpoints 3 clears all points from the third colourscale listscales Syntax void listscales Lists the current types colours and ranges of the colourscales 155 For example listscales removepoint Syntax void removepoint int scaleid int pointid Remove a single point from the selected colourscale For example removepoint 1 4 deletes the fourth point from colourscale 1 scalename Syntax string scalename int scaleid string scalename int scaleid string newname Retrieves the name of the colourscale id provided or sets the name if a new name is provided The name is displayed next to the gradient bar if drawn For example scalename 1 Orientation renames the first colourscale to Orientation scalevisible Syntax void scalevisible int scaleid bool visible Sets whether the gradient bar for the specified colourscale should be drawn in the main view Default is off for all colourscales For example scalevisible 9 yes 156 draws the gradient bar for the 9th colourscale in the main view setpoint Syntax void setpoint int scaleid int pointid double value double r double g double b double a 1 0 Sets the value and colour of an existing point in the specified colourscale For example Seirjooume il 2 3037 sO sO 1 OY sets the second point on colourscale
150. e to apply to the cell CylinderZ SlabYZ Slab in YZ Plane Number of partitions 2 Sphere Simple spherical region Number of partitions 2 a Cylinder along Z Axis Mn Number of partitions 2 SlabXY Slab in XY Plane Number of partitions 2 SlabXz Slab in XZ Plane Number of partitions 2 A Options for scheme SlabXZ Y X A pu Sikia Start Y 0 40000 End Y 1 00000 lt Back Next gt Cancel 9 ox Cancel Now we choose the partitioning scheme for the system We could be lazy and just choose None since the NaCl lattice should reject any water molecule we attempt to add over it However here we will choose an appropriate partitioning scheme for the task SlabXZ This will allow us to restrict water molecules to a specific y range in the unit cell Select SlabXZ and press the Scheme Options button to bring up the options dialog for the scheme There you will see the start and end values of y for the slab in fractional cell coordinates The initial minimum limit of 0 4 is luckily appropriate for the system but the upper bound needs to be set to 1 0 Press OK when done and then Next g Disorder Wizard y Y YY g Disorder Wizard y YA Step 4 5 Choice of Components Step 5 5 Set Component Populations Select the models representing the components to be added to the cell Set the desired population number and or density for each component Select models to use as components
151. e unit cell For example OLCHA foldmolecules Syntax void foldmolecules Fold all pattern molecules so the are unbroken across cell boundaries For example foldmolecules millercut Syntax void millercut int h int k int 1 bool inside FALSE Remove all atoms from the unit cell that lay outside the specified Miller plane and its mirror if it has one If the final parameter is given as TRUE then atoms inside the bounding Miller plane s are selected For example in ec il gt Ap de SAID e 149 removes all atoms inside the two enclosing 121 planes pack Syntax void pack Perform spacegroup packing on the current model For example pack printcell Syntax void printcell Prints the cell parameters of the current model For example printcell replicate Syntax void replicate double negx double negy double negz double posx double posy double posz Create a supercell of the current model creating copies of the cell in each of the three cell axis directions The number of cells to replicate in each positive and negative direction are specified as additional cells beyond the original So repoliceres 0 0 0 0 0 0 will do nothing at all to the model while Solicita 0 O dy 0 0 will result in a supercell that consists of eleven copies of the original cell along the x axis direction Simil
152. ection of atoms is possible from the measure toolbar Geometry o x Measure Distance Angle Torsion Ti Distance Ti Selection e Angle e Selection f Torsion I af Selection XK Clear Al Figure 7 21 Geometry Window Measure page Distances angles and torsions between atoms can be measure here select the desired tool on the left hand side and click the relevant number of atoms one by one in the main window Alternatively select a molecule or group of atoms for which you wish to measure all bound instances of a certain type of geometry and press the corresponding button on the right hand side To clear all measurements from the current model press the Clear All button Geometry o x Measure Distance Angle Torsion Current None no atoms selected New 1 08000 lt gt Y 2 lt gt D oh Nudge 1 00000 Figure 7 22 Geometry Window Distance page angle and torsion pages are similar The Distance Angle and Torsion pages of the Geometry window allow the specific geometry of a set of selected atoms to be set Simply select for example two atoms from a model note that they do not have to be connected by a bond and set or adjust their distance from here When choosing the Set Bond Length Set Bond Angle and Set Torsion Angle items on the atom context or Selection menu the Geometry window is automatically presented on the correct page for the number of selected atoms 78 7 15 G
153. ed J Build Open the Cell Define Window again and on the Spacegroup page enter the spacegroup as Cmc21 or 36 and press Set to assign the spacegroup to the model Then generate symmetry equivalent atoms by pressing the Pack button AG Aten vL7 r1671 Unnamed001 lt lt no filename gt gt Modified File Edit View Selection Model Trajectory Forcefield Settings Scripts Help Ve RABA Ne DA a oaa AXanwese e 3 lg ge la Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click 24 Atoms 144 120000 g mol drag or rotate in local frame right click drag ctrl remove from selection Orthorhombic 0 930293 g cm 34 Replicate Cell and Calculate Bonding The basic cell of ice I isn t particularly interesting by itself so we will replicate the cell to create a larger supercell and then calculate bonds in the new model so that the hexagonal structure is clear to see g Transform Build Script On the Cell Transform Window go to the Scale page and enter a scale factor of 5 628 for each of x y and z Press the Scale button to resize the unit cell Now select the Replicate page and enter positive replication values of 5 0 for both x and z and 2 0 for y and press Replicate to create the supercell Back in the Build Window go to the Edit page and Rebond the model A Aten vL7 r1671
154. ee http qt nokia com downloads Alternatively Qt4 is available on Fink qt 4 x11 If you re using the Fink installation of Qt4 then you ll also need pkg config from the same source 2 2 3 Configure Make Autotools Configure the source with the following commands run from the top level of the aten latest or aten nn mm directory bob pe gt autogen sh This creates the necessary files needed to properly configure the build If you unpacked the source from a tar gz it is not necessary to run autogen sh Next run the configure script to check for all programs and files that Aten depends on and set up the build If you plan on installing Aten properly i e install it on your machine so it is available to all users the configure script will place all binaries and necessary files in usr local by default This default location can be overridden by using the prefix lt path gt option So the plain command is bob pe gt configure To set the installation location use for example bob pe gt configur prefix home software On Mac OS X it is necessary to specify which Qt4 installation you have installed 1 e Framework or Fink bob pe gt configure with qt framework or bob pe gt configure with qt fink With the Fink installation you may also need to direct configure to the correct Qt4 development binaries either by setting your PATH to sw 1lib qt4 x11 bin PATH or by running
155. eed to have subversion http subversion tigris org installed since the GoogleCode repository where Aten lives is a subversion style repository To get yourself a copy of the latest source run the following command bob pc gt svn co http aten googlecode com svn trunk aten latest Afterwards you ll have a complete copy of the source in a directory called aten latest 2 2 2 Installing Necessary Pre requisites Aten has a fairly modest set of external dependencies namely Qt4 and readline Since you re building from source all the development files related to these packages must also be installed The C g compiler and the automake libtool packages are also a necessity Debian and Variants On deb based systems e g Debian and Ubuntu a command a bit like this should install all that you need bob pc gt sudo apt get install autotools dev libtool autoconf automake g libreadline5 dev libqt4 gui libqt4 opengl libqt4 core libqt4 dev RPM Based Systems For most other Linux flavours the method of installing the necessary software really depends a lot on your personal preferences or your system administrators For instance using zypper on an OpenSuSE distribution the command is run as root as follows bob pec gt zypper in readline devel libqt4 devel libtool automake Mac OS X On Mac OS X you have two ways of installing Qt4 Nokia offer an installable disk image providing Qt4 as a proper Framework s
156. eger Number of torsion terms defined in the forcefield 108 8 2 25 Forcefield Type Functions addangle Syntax ffbound addangle string form string type i string type j string type_k double datal Create a new angle definition in the forcefield See the angledef command for a full description addbond Syntax ffbound addbond string form string type i string type j double datal Create a new bond definition in the forcefield See the bonddef command for a full description addinter Syntax ffbound addinter string form int typeid double charge double datal Create a new interatomic definition in the forcefield See the interdef command for a full description addtorsion Syntax ffbound addtorsion string form string type i string type j string type k string type 1 double datal Create a new torsion definition in the forcefield See the torsiondef command for a full description addtype Syntax ffatom addtype int typeid string name string equiv stringlint element string neta string description Create a new type definition in the forcefield See the typedef command for a full description 109 finalise Syntax void finalise Finalise the forcefield See the finaliseff command for a full description findangle Syntax ffbound findangle string type i string type j string type k Search for an
157. el double x double y double z double vx 0 0 double vy 0 0 double vz 0 0 double fx 0 0 double fy 0 0 double fz Create a new atom in the model in fractional coordinates See the newatomfrac command for more details newbasisshell Syntax basisshell newbasisshell atom int i string type Create a new basis shell definition in the model centred on the specified atom id and of the given shell type See the newbasisshell command for more details 118 newbond Syntax bond newbond atom int i atom int j string int bondtype Create a new bond between atoms in the model See the newbond command for more details newbondid Syntax bond newbondid int id i int id j stringlint bondtype Create a new bond between atom IDs in the model See the newbondid command for more details neweigenvector Syntax eigenvector neweigenvector int size auto Create a new eigenvector in the model of the specified size If the size is not specified the vector length is set to match the number of cartesian basis functions store with the current basis shell definitions in the model See the neweigenvector command for more details newglyph Syntax glyph newglyph string style string options Create a new glyph in the model See the newglyph command for more details newgrid Syntax grid newgrid string name Create a new gridh in the model See
158. elds Window Forcefields page Energy Forcefields o x Energy Forcefields Manual Typing Manual Typing TypelD Name Description 4 1 _NDEF_ Set Clear Test Figure 7 19 Forcefields Window Manual typing page Assigning Atom Types Manual assignment of forcefield types can be performed in the Manual Typing page The list gives all atom types in the current forcefield that are relevant to the element entered just 74 above the list One can be selected from the list and be manually assigned forced onto the current atom selection with the Set button Such assignments will not be overwritten by subsequent automatic typings Manual typings can be removed with the Clear button and the currently selected atomtype can be tested for suitability on the current selection of atoms with the Test button 75 7 13 Fragments Window Fragments o x Group Fragment se v alkyl Methyl Y Adjust Bond Length on Paste Filter View As ShowAll Y List LJ Grid Figure 7 20 Fragments Window When in fragment drawing mode the Fragments window presents a list of all the available fragment models in either List or Grid formats and whichever is selected represents the current fragment to add in to the model The current fragment is attached to the mouse pointer when moving over the main canvas and shows a preview of what will be the orientation and position of the fragment when a left click is made If a fragment is
159. en the fourth and fifth atoms in the model newbond 1 2 3 creates a triple bond between the first and second atoms in the model APO E EEE EN 0 10 0 J newatom H 0 1 08 0 newbond 1 j single 138 creates a new single bond between two atoms supplied as references newbondid Syntax void newbondid int i int j void newbondid int i int j string int bondtype Create a new bond in the model between atoms referenced by their temporary ID set manually with the setid command Otherwise identical to the newbond command rebond Syntax void rebond Calculate bonding in the current model For example rebond rebondpatterns Syntax void rebondpatterns Calculate bonding in the current model but restrict bond creation to between atoms in individual molecules of defined patterns For example rebondpatterns rebondpatterns can be useful when molecules in a system are too close together to have the correct bonding detected In such a case bonds and any old patterns in the model may be cleared new patterns created by hand and then rebondpatterns used to calculate bonds only between the atoms of individual molecules in the defined patterns in order to recreate the original molecules For example Delete existing bonds in model clearbonds Delete any existing patterns in the model 139 clearpatterns Add new pattern 100 molecules
160. end of a character constant in the printf command does not implicitly mean and this is the end of the line you must indicate the end of the line yourself by placing W at the point where you wish the line to end So 283 cm IL ia y printf There would output Hello There Newlines An are an example of escaped characters the backslash indicates that the following character in this case n is not to be treated as a normal n but instead will take on its alternative meaning in this case a newline character There are one or two other escaped characters recognised see Escaped Characters for a list Note that the newline token can appear anywhere in the string and any number of times So cm MIO ata a 0 6 would output Hello There 11 3 2 Printing Data Being able to print simple text strings is good but not nearly enough The first argument to the printf command must always be a character string but any number of additional arguments may be provided Now these additional arguments may be number constants other character strings variables etc and may be output in the resulting string by referencing them with specifiers placed within the first example One example of a specifier is 3i which is shorthand for saying an integer value if used within the character string provided to printf the command will expect an integer constant or variable to be provided as an
161. energy forces are calculated C style format for atomic charge labels The far clipping distance used when rendering The near clipping distance used when rendering List of colourscales The current Colour Scheme used to colour atoms and bonds see Section 16 5 Lennard Jones parameter combination rule equations See Combination Rules in Section 16 6 for a list Comma separated list of common elements that appear in the Select Element dialog Whether to render solid or dashed rings for aromatics The unit of density to used when displaying cell densities Enables disables depth cueing The far fog distance used when rendering if depth cueing is enabled The near fog distance used when rendering if depth cueing is enabled The C style format to use for the numerical value of distance labels The electrostatic cutoff distance The method of electrostatic energy force calculation Arguments to pass to the movie encoder It should include the text strings FILES and OUTPUT will be replaced with a wildcard filelist and the output movie filename respectively Encoder executable including full path if necessary Set the unit of energy to use Update frequency for the energy in various methods Convergence parameter in Ewald sum Vector of Ewald reciprocal space vector limits kmax Precision parameter to use when generating parameters in EwaldAuto For spacegroups that are detected to have a hexagonal basis force packing to use gene
162. ent method as it is implemented in Aten converge Syntax void converge double econv double fconv Sets the convergence criteria of the minimisation methods Energy and force convergence values are given in the current working unit of energy in the program For example converge le 6 le 4 sets the energy and RMS force convergence criteria to 1 0E 6 and 1 0E 4 respectively linetol Syntax void linetol double tolerance Sets the tolerance of the line minimiser For example linetol le 5 205 sets the line tolerance to 1 0E 5 mcminimise Syntax void mcminimise int maxsteps Optimises the current model using a molecular Monte Carlo minimisation method For example mcminimise 20 runs a geometry optimisation for a maximum of 20 cycles Monte Carlo Minimiser method for details on the Monte Carlo minimisation method as it is implemented in Aten mopacminimise Syntax void mopacminimise string options BFGS PM6 RHF SINGLET Optimises the current model using the external MOPAC program Copyright 2007 Stewart Computational Chemistry Note that the program must be installed correctly as per the instructions provided with it and the path to the MOPAC executable must be set in Aten s preferences as well as a suitable temporary working directory The optional argument allows a specific MOPAC command to be provided for the minimisation but sensible def
163. ently visible Below the list the minimum and maximum data values contained within the grid and the current cutoffs i e the values for which the isosurface is drawn at for the primary and optional secondary surfaces to use when rendering the data The File and Edit menus allow new grids to be loaded into the current model and to cut paste and delete grids between models The Secondary checkbox specified that a second isosurface should be created for the current grid This is useful for instance to draw a second transparent surface at a lower cutoff than the primary or to display an isosurface encompassing the negated cutoff range of the primary e g to display both signs of the wavefunction in orbital data 80 Grids o x File Edit Data Cutoff Origin Axes Style Shift lt gt Axes x 0 00000 0 00000 0 00000 Y 0 00000 0 00000 0 00000 z 0 00000 0 00000 0 00000 Origin 0 00000 0 00000 0 00000 Figure 7 24 Grids Window Origin Axes page The associated origin and axes to the currently selected grid can be modified here In this way grid data may be arbitrarily flipped stretched and sheared and its position in the local space of the model changed All changes made are reflected immediately in the main view Grids o x File Edit Data Cutoff Origin Axes Style Shift lt gt Grid v Outline Volume 65 Periodic Colour From ColourScale Scale ID 1 unknown
164. er the master configuration should be demanded or whether the trajectory can itself be associated to any even an empty model Remember importtrajectory filters always attach the trajectory data to an existing model ImportTrajectory Filters An importtrajectory filter is written in a slightly different way to other filter types Since trajectory files may contain header data which is written once at the beginning of the file preceeding the frame data there are potentially two separate sets of data to read from trajectory files header data and individual frame data So rather than putting the code to read this data directly in the main body of the filter two functions should be defined instead 279 one for reading the header which must be called readheader and one for reading an individual frame which must be called readframe Note that if a given trajectory format does not contain a header the corresponding function may be left empty but must still be defined and should return a value of 1 Both functions take no arguments and must return an integer A template for an importtrajectory filter is thus filter type importtrajectory name Example Filter Template int readheader Code to read header data goes here int readframe Code to read frame data goes here The functions must take responsibility for informing Aten when the desired data cannot be read Both should return
165. ergy of the current frame of the trajectory associated with the current model For example 161 doubl nergy frameenergy modelenergy Syntax double modelenergy Calculate the energy of the current model which can then be printed out in whole or by parts by the other subcommands For example doubl modelenergy printelec Syntax void printelec Prints out the electrostatic energy decomposition matrix For example printelec printewald Syntax void printewald Prints the components of the Ewald sum energy For example printewald printinter Syntax void printinter Prints out the total inter pattern energy decomposition matrix 162 For example printinter printintra Syntax void printintra Prints out the total intramolecular energy decomposition matrix For example Pusiniteieleraca es printenergy Syntax void printenergy Prints the elements of the calculated energy in a list For example printenergy printsummary Syntax void printsummary Print out a one line summary of the calculated energy For example printsummary printvdw Syntax void printvdw Prints out the VDW energy decomposition matrix 163 For example printvdw veut Syntax double veut double veut double cutoff Return or set and return the cutoff radius
166. erse Power inversepower Uij rrij n Geom r Arith n 1 0 Arith Lennard Jones AB ljab Uij Arl12 Br6 A Geom B Geom UFF Lennard Jones ufflj Uy Diy or 12 n Di Geom 12 6 or O Geom n 2 0 Arith Buckingham exp6 buck Uy A ryB Cry A Geom 6 B Geom C Geom Morse morse Uij E0 1 exp k k Geom rij r0 2 1 r0 Arith E0 Geom Combination rule used to generate cross terms either Geometric or Arithmetic 316 13 2 Bond Functional Forms INET Ate Ignore Constraint Harmonic Morse Table 13 2 Bond Functional Forms Keyword Form ignore constraint Uij k2 r r0 2 harmonic Uij k2 r r0 2 morse Ui E0 1 exp B rij r0 2 317 13 3 Angle Functional Forms INET Ate Ignore Harmonic Cosine Double Cosine Harmonic Cosine Constraint 1 3 Bond Table 13 3 Angle Functional Forms Keyword ignore harmonic COS cos2 harmcos bondconstr aint Form Uy k2 0 00 2 Uyk k 1 scos n0 00 Uijk k C0 C1cos 0 C2 cos 20 Uy k2 cos 0 cos 80 2 Uy k2 r r0 2 318 Param s 1 0 13 4 Torsion Functional Forms Table 13 4 Torsion Functional Forms Name Keyword Form Param Cosine Cos Ugp k 1 scos n Qeq lt n peq s 1 0 Triple Cosine cos3 UQp 12 k1 1 cos p k2 1 cos 20p n k3 1 c0s 3p k3 Quadruple cos4 Up 12 k1 1 cos p k2 1 cos 20p kl Cosine k3 1 cos 3M k4 1 cos 4 k3 k4 Triple Cosine cos3c y p k0 12 k1 1 cos p k2 1 cos KO Constant KI 2p k3 1 cos 3
167. es in Aten that are of reference type i e the non standard types various sub variables and functions may be accessed in the same way class members are utilised in C Each non standard variable type is listed here along with the types and descriptions of their available subvariables members In the same way that class members are accessed in C C subvariables of reference types are accessed by use of the full stops between member names For instance the atom type allows all the information of a given atom to be accessed The following example illustrates the process of retrieving the third atom in the current model finding its coordinates and subsequently adjusting them atom a aten model atoms 3 vector v a r penne MOL orcas ces Sie tae un op Wwewyp Wo 9 as gt O a r v printf New coordinates are f f f n a rx a ry a rz Lots of paths are used here Firstly the global at envariable is used to get access to the current model and grab a reference to its third atom aten model atoms 3 Then the coordinates of this atom are placed in a vector v by requesting the r subvariable from the stored atom reference We then adjust the vector and store the new coordinates in the atom All members can be read but not all can be written back to these are read only members for which setting a value makes no sense Members which can be modified are indicated with mark in the RW column in the following tables
168. es that the script file is to be loaded and run before moving on to the next command line argument A script file is just a plain text file that contains sequence of commands to be executed written in the command language style see Section 8 1 string lt name value gt Creates a floating string variable name See the double switch for a full description T t lt file gt trajectory lt file gt Associates a trajectory file with the last loaded current model U u lt nlevels gt undolevels lt nlevels gt Set the maximum number of undo levels per model or 1 for unlimited the default Vv v verbose 51 Switch on verbose reporting of program actions vbo Attempt to use OpenGL vertex buffer objects when rendering for maximum performance Z z lt maptype gt zmap lt maptype gt Override the names to elements z mapping style defined in file filters For a list of possible mapping types see ZMapping Types in Section 16 16 6 3 Batch Processing Modes Aten has several batch or offline processing modes that do not need the GUI to be invoked These permit calculations analyses or processes to be performed on multiple models in one simple command Most work by storing any commands or command sequences supplied with command until all models are loaded and then running the commands on each loaded model in sequence The modes are as follows Batch Mode Invoked by the
169. es the number of Angstroms moved along the axis in each step For the cell reference frame it defines the fractional cell distance moved in each direction Position O Centre Flip Translate Shift Reposition Vector X 0 000000 gt Pick Y 10 000000 fio Normalise Z 0 000000 Magnitude 0 0 Shift 1 000000 da Figure 7 31 Position Window Shift page The vector along which to move the current selection is defined on the left hand side of the Shift page Furthermore the axis may be defined by Picking two atoms in the main window The supplied vector does not need to be normalised but thus may be performed through the Normalise button The defined shift value dictates the multiple of the defined vector by which selected atoms are shifted 85 Position o x Centre Flip Translate Shift Reposition Reference Target x 0000000 0000000 gt Y 0 000000 gt Y 0 000000 0 Z 0 000000 Z 0 000000 Define Define _ Reposition Figure 7 32 Position Window Reposition page The reposition page allows the centre of geometry of a selection of atoms to be moved from a reference coordinate defined by the Reference panel to a destination coordinate defined by the Target panel Either coordinate may be set from the centre of geometry of the current atom selection by pressing the relevant Define button 86 7 19 Select Window The select window provides a means to quickly access the
170. es within files can be made to attempt to identify them Individual strings can be given to the search keyword and may be specified multiple times The default is to search the first 10 lines of the file for one or more of the defined search strings but this can be changed with the within property For example search UberCode Version 20 0 matches the filter to any file containing the string UberCode Version 20 0 within its first 10 lines the default search SIESTA searches the first 10 lines of the file for the string SIESTA search GAMESS VERSION 11 APR 2008 R1 attempts to identify output from a specific version of GAMESS US type Syntax type filtertype The type keyword must be provided an all filter definitions an error will be raised if it is not It specifies which class of data the filter targets e g models grid data etc and whether it 1s an import or export filter A given filter may only have one type specified for which the possible values are Table 11 2 Filter Types Type Description exportexpression Describes how to export forcefield descriptions expressions for models exportgrid Describes how to export grid style data exportmodel Describes how to write out model data exporttrajectory Filter suitable for the export of trajectory data importexpression Describes how to load in forcefield style expressions importgrid Describes how
171. esence of those particular atoms within the ring that is considered important Bound atom descriptions given inside the bracketed part should again be listed in order of decreasing complexity Multiple rings may be specified with separate ring keywords allowing the location of fused ring atoms 313 Table 12 13 NETA ring Keyword Examples Command Meaning ring size 6 C n 6 aromatic Benzene style carbon C ring size 6 C n 6 nh 2 Carbon atom in cyclohexane size Only relevant in the bracketed part of a ring keyword size requests the exact number of atoms comprising the cycle Note that this may be used independently of the implicit size suggested by the number of atom descriptions supplied or in conjunction with a partial list of atoms Table 12 14 NETA size Keyword Examples Command Meaning ring size 7 Specifies a 7 membered ring 12 6 1 Geometries These keywords requests that the target atom if specified in the root of the type description or a bound atom if used inside the associated bracketed part should possess a certain physical geometry in terms of its connections The number of bonds to the target atom and the angles between them are used to determine the geometry Note that for some geometry types there are several ways for the atom to have this geometry unbound An unbound atom i e one with zero bonds to other atoms Only makes sense when used in the root of a type descrip
172. etupcomponent density 2 0 1 0 newmodel fcc cala aL 1 900 00 510 7 newatom Na 0 0 0 newatom Na 0 5 0 newatom Na 0 5 0 newatom Na 0 0 5 selectall copy paste flipx transmute Cl scale 5 628 5 628 5 628 rephicate 0 0 03 29D p SGuUASLIL MS n2 disorder SlabXZ end 1 0 0 5 5 5 0 0 32 5 4 Building Ice I from Crystal Information GUD Similar in spirit to the alumina example Section 5 2 here we create a single ice I crystal from the crystal information and then replicate it to form a larger supercell The crystal information used below is from Leadbetter et al J Chem Phys 82 424 1985 Table I Structural parameters of ice at 5 K Create the Basic Unit Cell First we create the unit cell which from the paper is orthorhombic with side lengths a 4 5019 b 7 7978 and c 7 328 A There a five symmetry unique atoms to add into the cell This might seem odd given that this doesn t add up to a whole number of water molecules but one of the water molecules lays with its oxygen on a mirror plane and so only needs one hydrogen to be specified Atom positions in the paper are given in fractional coordinates we will create the atoms using these coordinates which will be converted by Aten into their real cell coordinates automatically Define Open the Cell Define Window Add a unit cell to the model by checking the Has Cell Checkbox then go to the Def
173. eturns a string formatted according to the supplied format uppercase Syntax string uppercase string source Returns the source string with all lowercase letters converted to uppercase 245 9 29 System Commands System commands for controlling debug output instantiation of the GUI and exiting from the program debug Syntax void debug string type Toggles debug output from various parts of the code A full list of valid types is given in output types For example debug parse getenv Syntax string getenv string variable Retrieves the contents of the named environment variable so that transfer of useful quantities can be made to Aten through a shell For example string s getenv HOSTNAME gets the name of the host Aten is running on although what you would then usefully do with it I don t know Better examples can be found in the resources section of the website getenvf Syntax double getenvf string variable Retrieves the contents of the named environment variable converting it to a floating point double value in the process For example 246 double d getenvf num gets the shell variable num as a real number getenvi Syntax int getenvi string variable Retrieves the contents of the named environment variable converting it to an integer value in the process For example int i getenvi count ge
174. evant definitions are not already defined in the forcefield and the UFF and DREIDING forcefields contain no pre defined intramolecular terms whatsoever defines Syntax defines definename NETA string end The defines block makes it possible to state commonly used or lengthy chunks of NETA that do not belong to any specific atom type and which can then be reused multiple times in many different atom type descriptions Each definition in the block is given an identifying unique name which allows it to be referenced with the symbol The NETA descriptions provided for each definition must be valid or the forcefield will not be loaded In subsequent NETA definitions for atom types the definitions may be inserted by stating definename For example defines water oxygen 0 nh 2 nbonds 2 end types il HW2 H nbonds 1 water oxygen Water hydrogen end equivalents Syntax 296 equivalents alias typename typename end In forcefields the most detailed information provided is typically the short range intermolecular and charge parameters with different values or at least different charges given to each individual atom type Usually intramolecular terms are more general and don t depend so much on the exact atom type For example given a tetrahedral carbon CT and three different aliphatic hydrogens H1 H2 and H3 the bond between the carbon and any of the three hydrogen types will likely be the
175. existing angle definition in the forcefield between the type names supplied findbond Syntax ffbound findbond string type i string type j Search for an existing bond definition in the forcefield between the type names supplied findimproper Syntax ffbound findimproper string type i string type j string type k tring type 1 n Search for an existing improper torsion definition in the forcefield between the type names supplied findtorsion Syntax ffbound findtorsion string type 1 string type j string type k string type l Search for an existing torsion definition in the forcefield between the type names supplied findureybradley Syntax ffbound findureybradley string type i string type j string type k Search for an existing Urey Bradley definition in the forcefield between the type names supplied 110 8 2 26 Glyph Type The glyph type contains information describing a single glyph within a model Table 8 16 Glyph Type Members Member Type RW Description data glyphdata Individual data for each vertex of the glyph ndata int How many data points vertices are associated with this glyph s type rotated int Flag to indicate whether the glyph s rotation matrix has been modified i e the glyph has been rotated Setting this to 0 resets and removes any current rotation matrix same as calling member function resetrotation rotation double 9 Rotation
176. ffect others There are some issues with the Qt code used to grab the current view as an image but an alternative method is available and works Try the prefs option aten prefs useframebuffer TRUE to use the alternative method If this remedies the problem add the line to your preferences file One caveat although this appears to fix problems when saving images from the GUI it does not apparently solve the problem when saving the image from the command line ALL Why is Aten s main view corrupt black I can t see anything This is a fairly common issue and the exact causes are not known for sure Certainly on some Linux machines the presence of an ATI graphics card seems to be related Using the radeon or fglrx drivers supplied with the OS rather than the proprietary ati driver sometimes helps Forcing the main view widget to manually refresh itself usually solves the problem To do this on the latest versions activate Settings Manual Swap Buffers from the main menu on newer versions or type the following into Aten s command window aten prefs manualswapbuffers TRUE If this remedies the problem add the line to your user preferences file see Section 4 2 2 WINDOWS Aten fails to start giving this message 13 C Program Files Aten 1 7 1635 bin Aten exe Q C Program Files Aten 1 7 16351bin Aten exe This application has failed to start because the application configuration is incorrect Reinstalling the
177. folded back in to the confines of the cell If the Prevent Folding checkbox is ticked these folding operations will not occur 63 7 8 Cell Definition Window Allows the user to edit the unit cell specification of the current model assign a crystallographic spacegroup and perform spacegroup packing according to the spacegroup Whether or not the current model possesses a unit cell is determined wholly by the Has Cell checkbox if checked the current model is periodic if not then it is an isolated collection of atoms Cell Definition o x Cell Definition o x V Has Cell Has Cell Matrix Define View ABC Spacegroup Matrix Define View ABC Spacegroup X 10 000000 0 0000000 0 0000000 gt Lengths Angles Y 0 0000000 amp 10 0000001 4 0 0000000 a 10 00000000A a 90 00000010 Z 0 0000000 0 0000000 10 000000 amp b 10 00000000 B 90 00000010 Y c 10 00000000 90 00000010 Define Volume 1000 000 A Volume 1000 000 A Figure 7 7 Cell Definition Window Matrix and Define View pages If the model has a cell its size and shape can be set in one of two ways The primary method 1s though direct editing of the cell matrix on the Matrix page which presents the individual components of the X A Y B and Z C axes All values are in Angstroms and any changes made here are immediately applied to the current model Alternatively the cell may be set by entering its lengths in Angstr
178. form double ax double ay double az double bx double by double bz double cx double cy double cz double ox double oy double oz Transform the current selection by applying the defined matrix to each coordinate operating about the supplied origin or 0 0 0 by default No orthogonalisation or normalisation of the defined axes is performed For example mara ns WO 0 O I 0 0 0 1 does absolutely nothing multiplying by the identity matrix Metas lO O 0 il 0 O O ijs mirrors the current selection in the xy plane ci ecc ion De O O 03 OF Or Os scales the x and y coordinates of all selected atoms by 0 5 leaving the z coordinates intact reorient 254 Syntax void reorient atom int i sx atom int j sx atom int i sy atom int j sy atomjint i sz atom int j sz double t ax double t_ay double t_az double t_bx double t_by double t_bz doubl t_cx double t_cy double t_cz 0 void reorient atom int i sx atom int j sx atom int i sy atom int j sy atom int i sz atom int j sz double t ax double t ay double t az double t bx double t by double t bz double t_cx double t_cy double t_cz double ox double oy double oz Operates in exactly the same manner as matrixtransform except that the source matrix is defined from atoms or their IDs and the destination matrix is provided as a matrix setangle Syntax void setangle a
179. g the control type string in the option command Table 11 3 Option Types Type Required Data Description check int state A checkbox whose state is either off or on Returns an integer value 1 if the control is ticked 0 otherwise The initial state 0 or 1 is supplied combo string items A combobox is a drop down list of predefined int default items supplied as a comma separated list The default item selection should be provided as in integer index The text of the selected item is returned doublespin double min Control allowing a real number to be input strictly double max within the min max range and with start value double step specified Up down arrows to the side of the double start control adjust the current value by the step value 275 A real number is returned edit string value intcombo string items Exactly the same as the combo control above but int default instead returns an integer value corresponding to the index of the selected entry intspin int min Control allowing an integer number to be input int max strictly within the min max range and with start int step value specified Up down arrows to the side of the int start control adjust the current value by the step value An integer number is returned label None A simple text label with no associated value radio string group A radio control is part of a set of checkable items int checked of which only one can be selected at an
180. g types can be determined Rings are classed as either aliphatic aromatic or non aromatic i e a mix of resonant and aliphatic bonds that is not itself aromatic Now working only with the representative molecule of each pattern associated or current forcefield s are searched for types that match the contained atoms Each NETA description whose character element is the same as a given atom is tested and a score is obtained If this score is non zero and positive then the atomtype is a match and is assigned to the atom if it has no previous type or if the score is higher than the previous one See atom type scoring in Section 12 5 3 for more information 1 Pedretti A Villa L Vistoli G Theoretical Chemistry Accounts 709 229 232 2003 15 1 2 Augment Augmentation of bonds as far as Aten is concerned means to take a collection of atoms with basic connectivity 1 e all single bonds as per the result of rebonding and assign multiple bonds where necessary The method is based loosely on previously described algorithms 1 The basis of the method involves modifying the bond order of a particular connection to best satisfy the bonding requirements of the two involved atoms for example making sure all carbon atoms possess an optimal total bond order of 4 However many atoms in particular S and P happily exist with more than one total bond order e g P the methodology borrowed from 1 solves this problem by scoring the t
181. he basis shell primitives basisprimitive List of primitives defined for the basis shell type string The type shape of the basis shell See Basis Shell Types in Section 16 1 for a list 8 2 9 BasisShell Type Functions addprimitive Syntax basisprimitive addprimitive double exponent double coeffl 0 0 Add a new primitive to the basis shell with the specified exponent and optional coefficients given 8 2 10 Bond Type The bond type represents a chemical connection of some defined order between two atoms Table 8 6 Bond Type Members Member Type RW Description 1 atom First atom involved in the bond atom Second atom involved in the bond order double Bond order type string Bond Type see Section 16 2 for a list 8 2 11 Bond Type Functions partner Syntax atom partner atom i 103 Return the other atom i e not i involved in the bond 8 2 12 Bound Type The bound type is used by the pattern type and defines a single bound interaction e g a bond angle or torsion between a group of atoms within the pattern It differs from the f fbound type since no forcefield information is stored locally in the structure Table 8 7 Bound Type Members Member Type RW Description data double Parameters describing the bound interaction escale double Electrostatic 1 4 scaling factor for torsion interactions form string Functional form of the bound interaction id int Array of at
182. he original variable Hence in the example given above after the termination of the block the final printf statement again sees the original variable i complete with its initial value of 99 intact Note that if a variable is re declared within a scoping block there is no way to access the original variable until the scoping block has been closed Blocks can be nested to any depth 8 1 6 Functions For functions that take arguments the argument list should be provided as a comma separated list in parentheses after the function name For instance NAC ial O 2 Arguments may be constant values as in this example variables arithmetic expressions or any other function that returns the correct type For functions that optionally do not take arguments the empty parentheses may be omitted A list of all functions their arguments and their return types is given in the command reference in Section 9 All functions return a value even if it is no data i e void in C C For instance in the example above the newatom command actually returns a reference to the atom it has just created and this may be stored for later use ceon ey EE MEE AE O sO 0 However if the return value of any function is not required then it may simply be forgotten about as in the example prior to the one above 8 1 7 User Defined Functions 97 User defined functions can be defined and used in Aten taking a list of variable arguments w
183. he source string that comes after the first occurrence of the search string If source doesn t contain any occurrences of search an empty string is returned unless the flag sourceonfail is set to TRUE in which case the original source string is returned instead For example string fullname BobBobbinson string firstname afterstr name Bob sets the variable firstname to the value Bobbinson string textl text2 textl No taxes on axes text2 afterstr textl x results in text2 having a value of es on axes atof Syntax double atof string text Converts the supplied text into its floating point double representation Equivalent to the standard C routine atof For example double x atof 1 099d would set x to the value 1 099 atoi 241 Syntax int atoi string text Converts the supplied text into its integer representation Equivalent to the standard C routine atol For example nee Lo OOO ZAS y would set i to the value 23 beforestr Syntax string beforestr string source string search bool sourceonfail FALSE Return the part of the source string that comes before the first occurrence of the search string If source doesn t contain any occurrences of search an empty string is returned unless the flag sourceonfail is set to TRUE in which case the original source string is returned instead For example
184. he specifed parameter of the given functional form The form and related parameter should correspond to those given in the VDW functional forms table A string corresponding to one of the available combination rule options is returned For example 174 string cr getcombinationrule 13 epsilon getff Syntax forcefield getff string name E orcefield getff int id Select the named forcefield or forcefield with the specified id and make it current returning a reference to it in the process For example forcefield uff getff uff makes the loaded forcefield named uff the current one and stores a reference to it interdef Syntax void interdef string form int typeid double charge double datal Add a new short range data definition to a type in the current forcefield form should correspond to one of the implemented VDW functional forms Up to ten parameters for the VDW potential may be given loadff Syntax forcefield loadff string file string name Load a forcefield from file and reference it by name Becomes the current forcefield For example loadff home foo complex ff waterff loads a forcefield called complex ff and names it waterff map Syntax 175 void map string map Set up manual typename mappings for atom names that do not readily correspond to element symbols forcefield types etc All atoms that are s
185. hoes of useful Fortran features included for good measure This means that if you re familiar with C C then controlling Aten from the command line or writing a script command or filter should be relatively straightforward There are lots of C primers on the web so the following sections provide only a brief summary of the style of the language 8 1 1 General Input Style Keywords variables and function names are case sensitive so for is different from For all internal commands in Aten are in lowercase Individual commands must be separated by a semicolon and newlines are optional For example ime te primor Wiello tiere np i 5 and bala LA printf Hello there n a gt 50 are equivalent Whitespace characters spaces and tabs are ignored and may be present in any amount in any position in the code Individual lines or parts of them may be commented out The presence of either the hash symbol or in a line means ignore rest of line Note that the commenting style 1s not supported 8 1 2 Variables There are several standard rules for variables within Aten e They must be declared before use e They are strongly typed i e they hold a specific type of value e g an integer a character string etc e They must begin with an alpha character a to z but may otherwise consist of letters numbers and the underscore _ e They may not be named the
186. hydrogen command for more details angleenergy Syntax double angleenergy Calculates and returns the total angle energy for the current model augment Syntax void augment Automatically detect and add multiple bonds in the system See the augment command for more details bondenergy Syntax double bondenergy 115 Calculates and returns the total bond energy including Urey Bradley contributions for the current model charge Syntax void charge Assign charges to the model from the current forcefield See the charge command for more details clearbonds Syntax void clearbonds Remove all bonds from the model See the clearbonds command for more details clearcharges Syntax void clearcharges Remove al charges from the model setting them to zero See the clearcharges command for more details clearselectedbonds Syntax void clearselectedbonds Remove all bonds from the current atom selection See the clearselectedbonds command for more details copy Syntax void copy Copy the current atom selection to the clipboard See the copy command for more details cut Syntax void cut 116 Cut the current atom selection to the clipboard See the cut command for more details delete Syntax void delete Delete the current atom selection See the delete command for more details elecenergy Syntax
187. ible options For example addreadoption stripbrackets eof Syntax int eof Returns 1 if at the end of the current input file O otherwise For example Scale SA ile cs Lecce e s ar Mesa sp Reads in and prints out all lines in the current source file 219 filterfilename Syntax string filterfilename Returns the name of the current input or output file typically useful from within an import or export filter For example string filename filterfilename Puts the current source destination filename in the variable filename find Syntax int find string searchstring int find string searchstring string linevar Searches for the specified searchstring in the input file returning 0 if searchstring is not found before the end of the file and 1 if it is The optional argument linevarisa character variable in which the matching line if any is put If the search string is not found the file position is returned to the place it was before the command was run For example int iresult find Final Energy searches for the string Final Energy in the input file placing the result of the search in the variable iresult string line int n find Optimised Geometry line searches for the string Optimised Geometry in the input file placing the whole of the matching line from the input file in the variable line getline Syntax
188. ick Angle 60 00000 0 Figure 7 35 Transform Window Axis Rotate page The Rotate page allows an origin and a rotation axis about this origin to be defined about which to rotate atom selections The origin and axis may be entered manually can be determined from a current atom selection Define buttons or defined by the click selection of two atoms Pick button Defining the rotation axis from the current selection will set the axis to the vector between the currently defined origin and the centre of geometry of the current atom selection Rotations of atom selections about this axis origin combination are then made by defining the Angle of rotation in degrees and then applying the rotation either clockwise or anticlockwise 90 Matrix Transformation Atom Transform o x Axis Rotate Transform Matrix Convert Matrix X 1 00000 0 00000 0 00000 0 Y Pick fio Nom big Ortho IRE Gen Y 0 00000 9 1 00000 0 00000 Figure 7 36 Transform Window Transform page From here a 3x3 transformation matrix can be applied to the current atom selection and with a specific coordinate origin not necessarily the centre of geometry of the selection The Pick buttons allow selection of the various axes through click selection of two atoms not necessarily in the same model as the current atom selection while the Normalise buttons will normalise each of the currently defined axes to be of unit
189. ill be read from the source file and returns it as an integer value representing the ASCII character code see http www asciitable com for example The actual file position for reading is unaffected For example int char peekchari readchars Syntax GI string readchars int nchars bool skipeol TRUI Reads and returns as a string a number of characters from the input file If skipeol is true the default then the end of line markers Wn and r will be ignored and will not count towards nchars this is of most use when reading formatted text files and you want to ignore the fact that data is presented on many lines rather than one If skipeo1 is false then n and r will count towards the total number of characters Used on formatted text files this might give you unexpected results For example string text readchars 80 reads the next 80 characters from the input file and puts it into the variable text readdouble Syntax double readdouble double readdouble int nbytes Read a floating point value the size determined from the machines double size from an unformatted binary input file Alternatively if a valid number of bytes is specified and corresponds to the size of another class of double e g long double on the machine this size is used instead For example double x readdouble reads a floating point value into the variable x readdoublearr
190. ilter option is defined in the following way within a filter file vartype var option string name string type The specified name is the text that will appear next to the control in the GUI The type of control governs the type of GUI widget that will appear see the list of types in Table 11 3 below Following these two mandatory specifications any required values must then be given in the correct order after which any other non control specific options may be given each surrounded by quote marks and in the format option or option value All of these are to do with the layout of controls see the option layout section For example we we can set a string variable with one of several possible values using a combo box control in the GUI When saving a file in a new format or by selecting Export Options from the File menu a dialog is shown in the GUI which contains all of the defined controls in the relevant filter from which options can be set before the file is written This would be written as follows in the filter file string runtype option Run Type combo check run restart analyse 2 Note that when the filter code actually runs the target variable runt ype will be set with whatever value the control holds in the GUI or the default if running from the command line no questions are asked interactively at the points at which the option statements exist So the variable here will be guaranteed to take on one of
191. ine View ABC page and set the cell lengths a b and c to 4 5019 7 7978 and 7 328 respectively Leave the cell angles all at 90 and click Define Y Build In the Build Window change the active element on the Edit page to oxygen by clicking the E button On the Add Atom panel in the Tools page make sure Fractional Coordinates is checked and then enter the following sets of coordinates clicking Add after each set is entered x 0 0 y 0 6648 z 0 0631 x 0 5 y 0 8255 z 0 0631 Go back to the the Edit page and change the active element to hydrogen by clicking the LJ button Then return to the Tools page and add three more atoms at the following fractional coordinates x 0 0 y 0 6636 z 0 1963 x 0 0 y 0 5363 z 0 0183 x 0 6766 y 0 2252 z 0 0183 33 AG Aten vL7 11671 Unnamed001 lt lt no filename gt gt Modified Ya x File Edit View Selection Model Trajectory Forcefield Settings Scripts Help DAX De RAit tomfosae2Ranee Oy el e Select Click or click drag to select shifttogale left click or add area to selection left click drag or translate middle click 5Atoms 35 022000 g mol drag or rotate in local frame right click drag ctrl remove from selection Orthorhombic 0 226067 g cm Set the Spacegroup and Pack To complete the model the spacegroup of the crystal must be set so that generation of the symmetry related atoms can be perform
192. ing exactly the same procedure Second Stage Augmentation The above two steps are enough to correctly determine multiple bonds in a chemically correct molecule provided no cyclic moities are present in the system The second stage is designed to correct improper augmentations within cycles or shift existing augmentations around cycles such that other missing multiple bonds may be created For each existing multiple bond in each cyclic structure in each pattern s molecule a simple re augmentation of the constituent bonds is first attempted in order to try and lower the total bond order score for the whole ring i e the sum of the individual bond order scores of every atom present in the cycle Then each bond in the ring is considered in sequence If the bond is a double bond then we attempt to convert this into a single bond and make the two adjacent bonds in the ring double bonds in an attempt to aromaticise the ring The total bond order score is checked and if lower than the previous score the change is accepted If not the change is reversed and the next bond is considered By performing these secondary adjustments the double bond pattern of many complex poly aromatics can be correctly and fully automatically detected 1 Automatic atom type and bond type perception in molecular mechanical calculations J Wang W Wang P A Kollman and D A Case Journal of Molecular Graphics and Modelling 25 2 247 260 2006
193. ining the type Z int Element id Z corresponding to the target element of this type 8 2 21 FFAtom Type Functions datad Syntax double datad string varname Return the value of the defined data item varname as a double if it has been defined in a data block in its encompassing forcefield datai Syntax int datai string varname Return the value of the defined data item varname as an integer if it has been defined in a data block in its encompassing forcefield datas Syntax string datas string varname Return the value of the defined data item varname as a string if it has been defined in a data block in its encompassing forcefield parameter Syntax double parameter string name Return the value of the parameter name in the associated vdW data See VDW Functional Forms in Section 13 1 for a list of parameter names in the supported vdW functions 8 2 22 FFBound Type 107 The f fbound type stores parameter data relevant to a specific bound interaction within a pattern It differs from the bound type in that no atom ID information is stored Table 8 14 FFBound Type Members Member Type RW Description data double Parameter data for the potential datakeyword string Keyword names of the associated parameters up to nparams datanames string Proper names of the associated parameters up to nparams escale double For torsion type interactions the electrost
194. ion be present and one is automatically created as and when necessary See Section 10 3 for more information Filter A filter is a set of commands i e a program which loads data in to or saves data from Aten Aten depends on filters to be able to load and save models forcefields expressions trajectories and grid data All filters are written in Aten s own scripting language which is based syntactically on C and are loaded in on startup New filters can be added at will by the user to cater for specific formats See Section 11 for more information Expression While a forcefield is a collection of terms bonds angles van der Waals terms etc which describe usually a large number of molecular types and systems an expression is a subset of terms specific to one model NETA Aten is able to automatically assign forcefield atom types to atoms in a model through the use of type descriptions in the Nested English Typing of Atoms NETA language This is a simple readable system for describing the connectivity and environment of individual atoms See Section 12 5 for more information Fragment A fragment is a molecule or structure which can be used to quickly build up a new model or modify an existing one For example cyclohexane or a tertiary butyl group 15 4 2 File Locations 4 2 1 Installed Provided Files Aten depends on several sets of files in order to function properly and generally speaking knows where t
195. is written to a variable first and then the file writevarf Syntax void writevarf string dest string format Write to the supplied string variable dest the string resulting from the supplied format and any other supplied arguments Apart from the mandatory first argument being the destination string variable usage is otherwise the same as the printf command Note that a newline character is not automatically appended to the end of the written line and one should be written explicitly using the escape sequence n For example string s writevarf s s 8i n Number of atoms aten model natoms writeline s same result as the example for the writelinef command except that the final string is written to a variable first and then the file 228 9 25 Script Commands Commands to load and run scripts listscripts Syntax void listscripts Lists all loaded scripts For example ILL SHE Reraljones 7 loadscript Syntax void loadscript string filename void loadscript string filename string nickname Loads a script from the filename specified giving it the optional nickname For example loadscript Scripts liquid water txt water loads the script from seripts liquid water txt and gives it the nickname water runscript Syntax void runscript string name Executes the specified script For example runscript water executes the
196. isible again 214 9 23 Monte Carlo Commands Change parameters for Monte Carlo based calculations Energy values should be given in the current working unit of energy in the program mcaccept Syntax void mcaccept string move double emax Sets the energy difference emax for the movetype move above which moves will be rejected For example mcaccept translate 0 0 requests that only translation moves that lower the overall energy will be accepted mcaccept insert 200 0 requests that insertion moves will be accepted provided the total energy does not rise more than 200 0 units mcallow Syntax void mcallow string move bool allow Indicates whether to allow moves of the specified type in Monte Carlo calculations For example mcallow translate FALSE disallows translation moves in Monte Carlo calculations mcallow rotate true allows rotation moves in Monte Carlo calculations mcmaxstep 215 Syntax void mcmaxstep string move double mcmaxstep Sets the maximal step size for the move type move For example mcmaxstep translate 5 0 sets the maximum translation displacement to 5 A mcmaxstep rotate 30 0 sets the maximum rotation to 30 degrees mcntrials Syntax void mcntrials string move double n Sets the number of times n that the move type move should be attempted in each cycle For example mentar lts MS SiS 01
197. itable expression is the process of taking a system of atoms and generating a prescription for calculating the energy and or forces arising from these interactions from any standard classical forcefield available Patterns describe systems in terms of their constituent molecular units For an N component system a single isolated molecule is a 1 component system there are N unique molecule types which are represented as ideally a set of N patterns Forcefield sub expressions can then be created for each pattern and applied to each molecule within it allowing the expression for the entire system to be compact and efficient Each pattern contains a list of intramolecular terms bonds angles etc atom types and van der Waals parameters for a single molecule that can then be used to calculate the energy and forces of M copies of that molecule 10 3 1 Determination of Patterns From the atoms and the connectivity between them Aten will automatically determine patterns for systems of arbitrary complexity The ordering of atoms is important however and the atoms belonging to a single molecule must not be interspersed by those from others In other words the atoms belonging to one instance of a molecule must be listed consecutively in the model There are also many ways to represent the same system of atoms all of which from the point of view of the program are equivalent and will produce the same total energies and atomic forces Consider th
198. ith optional default values The syntax for defining a function is as follows type name arguments commands type is one of the standard variable types and indicates the expected return value type for the function If no return value is required i e it is a subroutine rather than a function then type should be replaced by the keyword void void name arguments commands Once defined functions are called in the same way as are built in functions The name of the function obeys the same conventions that apply to variable names e g must begin with a letter cannot be the name of an existing keyword function or variable The arguments are specified in a similar manner to variable declarations A comma separated declaration list consisting of pairs of variable types and names should be provided e g WO Whe routines aime ab sligis aj Clowllolka stacicoxe jy ff soo Our new subroutine testroutine is defined to take three arguments two integers i and j and a double factor All three must be supplied when calling the function e g printf Calling testroutine n int num 2 double d 10 0 testroutine num 4 d printf Done n When defining the function subroutine arguments default values may be indicated and permit the function to be called in the absence of one or more arguments For instance lets say that for our testroutine the final argument factor is likely to be 10 0 on most occasions
199. jose oe Epio qe Tiberi ae Eppo oe A id Cfie Culic Sino o atic NO SC Tap This will take a few minutes Once complete build Qt with PS C qt 2010 05 qt gt nmake This will take a few more minutes approximately one hour depending on your system s speed 2 3 9 Download and Build Aten Go to www projectaten net download and get a zipped copy of the source For this example the latest beta version is 1 7 1626 so the zipfile is called aten 1 7 1626 zip Unpack the source somewhere here it has been placed in the users s home directory and run cmake to generate the necessary makefiles PS C Documents and Settings Your Name gt cd aten 1 7 1626 PS C Documents and Settings Your Name aten 1 7 1626 gt cmake G NMake Makefiles Then build Aten by running nmake PS C Documents and Settings Your Name aten 1 7 1626 gt nmake Time to wait again but hopefully after a little while you will see something resembling the following the important part is the 100 Built target Aten C Program Files Microsoft Visual Studio 10 0 VC INCLUDE stdlib h 433 see declaration of getenv C Documents and Settings Your Name My Documents aten 1 7 1626 src main cpp 52 warning C4996 getenv This function or variable may be unsafe Consider using _dupenv_s instead To disable deprecation use _CRT SECURE NO WARNINGS See online help for details C Program Files Microsoft Visual Studio 10 0 VC INCLUDE stdlib h 4
200. l files provided as arguments on the command line the specified model import filter is used to load them regardless of their filename extension or indeed actual format Since Aten tends not to determine file formats by looking at their content this is useful for when you know that file is in a particular format but with an extension that doesn t help Aten recognise it as such ff lt file gt Loads the specified forcefield file making it the current forcefield If the desired forcefield is present in either Aten s installed data directory or in your own aten ff directory see Section 4 2 then just the filename need be given as Aten searches these locations by default filter lt file gt Load the specified file as if it were a filter file installing any filters defined within it Any filters already loaded that have the same nickname id etc will be hidden by those loaded from file See Section 11 1 3 for more information on overriding existing filters fold Force folding of atoms to within the boundaries of the unit cell if one is present in loaded models even if the command fold was not used in the corresponding filter G g lt file gt grid lt file gt Loads the specified grid data file associating it to the current model and making it the current grid A model even an empty one must exist for a grid to be loaded H h help Show the possible command line switches and a shor
201. l unit of energy in use by Aten See also Energy Units Section 16 8 and the relevant prefs accessor findelement Syntax element findelement string name Convert the name specified into an element according to the current ZMapping Type Section 16 16 8 2 4 Atom Type The atom type encompasses a single atom in a model or frame Table 8 3 Atom Type Members Member Type RW Description bonds bond List of bonds the atom is involved in colour double 4 Custom colour of the atom used when the Colouring Scheme see Section 16 5 is set to custom data string Temporary character data stored on the atom for use in filters etc element element Returns a pointer to the assigned element data of the atom fixed int Whether the atom s position is fixed 1 or not 0 f vector Force vector fracx double Position x component in fractional cell coordinates fracy double Position y component in fractional cell coordinates fracz double Position z component in fractional cell coordinates fx double Force x component fy double Force y component 101 fz double Force z component hidden int Whether the atom is hidden 1 or visible 0 1d int Numerical ID of the atom within its parent model mass double Atomic mass of the atom name string Element name of the atom q double Atomic charge associated to the atom r vector Position vector rx double Position x component r
202. l x y z newatom el x y z The variables e1 x y and z will at any one time contain the element type and coordinates from one line of the file In an analogous manner the data may be written out again with the corresponding writeline command for atom i aten model atoms i i writeline i symbol i rx i ry i rz Each line will have the individual data items separated by a single space The readnext command reads in a single delimited item from a source file preserving the remainder of the input line for subsequent operations If there is no data left on the current line a new line is read and the first delimited item is returned The example above might be written in a slightly clunkier form as doublen yr Z Seha pelle while eof r readnext e readnext x readnext y z el I readnext z r r r newatom xX 1YrZ A For all delimited reading operations items of data read from the line are converted automatically into the type of the destination variable So the atom coordinates read in above which are put into double type variables could equally well be put into string variables Standard C routines are used to convert data items in this way and only some conversions make sense For instance attempting to read an item which is a proper character string such as element symbol name data into a double or integer variable does not make sense No error message will be raised and the
203. late camera Ctrl Click hold drag to translate selection in local model space 7 2 1 Manipulating the View At its most basic Aten s main view acts as a visualiser allowing models to be rotated zoomed in and out and drawn in various different styles By default the right mouse button is used to rotate the model in the plane of the screen right click and hold on an empty area of the canvas and move the mouse and the mouse wheel zooms in and out Note that right clicking on an atom brings up the atom context menu equivalent to main window s Selection menu The middle mouse button translates the model in the plane of the screen again click hold and drag These rotation and translation operate only the position and orientation of the camera with no modifications made to the actual coordinates of the model The view can be reset at any time from the main menu View Reset or by pressing Ctrl R Both the main menu View Style the main toolbar and the shortcuts Ctrl 1 to Ctrl 5 allow the drawing style of models to be changed between stick tube sphere scaled sphere and individual The last option allows different view styles to be set for different atoms 55 The Ctrl key changes the normal behaviour of the rotation and translation operations and forces them to be performed on the coordinates of the current atom selection instead of the camera The centroid of rotation is the geometric centre of the selected atoms T22 Atom
204. le 4 double 4 int 127 number of triangles used to generate primitive objects of the main view Higher values give rounder atoms but make rendering slower See also the imagequality setting Whether to fold atoms before cell replicate Whether to trim atoms after cell replicate Flag specifying whether to use the current rendering quality value when saving images FALSE or the imagequality value TRUE Multiple of the standard atom radius to use for transparent selection spheres The shininess of atoms value must be between 0 and 127 inclusive Colour of all specular reflections Whether the spotlight is on or off The ambient colour component of the spotlight The diffuse colour component of the spotlight Spotlight coordinates in A The specular colour component of the spotlight Line width of unselected stick atoms Line width of selected stick atoms Temporary working directory for some operations e g execution of MOPAC jobs Colour of rendered text Z width of individual transparency bins Whether sort of transparent triangles is enabled When enabled any object which is to be drawn in a transparent colour is split into its component triangles and sorted over several bins representing slices in the z direction Rendering is a little slower with this option enabled but corrects most transparency artefacts with sensible bin values The number of bins to use for sorting transparent triangles
205. lecule of the pattern nffangles int Number of unique angle terms used in the pattern nffbonds int Number of unique bond terms used in the pattern nfftorsions int Number of unique torsion terms used in the pattern nfftypes int Number of unique atom types used in the pattern nmolatoms int Number of atoms in one molecule of the pattern nmols Int Number of molecules repeat units in the pattern ntorsions int Number of torsion interactions in one molecule of the pattern torsions bound Array of torsion interactions in one molecule of the pattern 8 2 34 Pattern Type Functions atomsinring Syntax int atomsinring int id_ ine tda gp Sel 123 Return whether the supplied atom index indices given in local pattern atom numbering is in a ring the same ring cog Syntax vector cog int index Return calculated centre of geometry for the molecule index provided com Syntax vector com int index Return calculated centre of mass for the molecule index provided 8 2 35 Prefs Type The prefs type contains all preferences and settings information detailing the inner bits and pieces of Aten It exists as a single instance owned by and available through the aten master type Table 8 22 Prefs Type Members Member Type RW Description anglelabelformat string e The C style format to use for the numerical value of angle labels aromaticringcolour double 4 Colour of aromatic ring circles atomst
206. lexible specifications If used inside the bracketed part of a ring description this only indicates that the atom type should be present within the cycle the connection to the target atom is unimportant If used in a chain keyword the connection type is honoured Table 12 3 NETA X Keyword Examples Command Meaning H A single bond to a hydrogen atom amp 120 A single bond to an atom which matches type ID 120 see Reusing Types in section 12 5 4 C N A single bond to either a carbon or a nitrogen F Cl Br 1I At A single bond to any halogen atom amp 10 amp 11 amp 18 Kr A single bond to an atom with type ID 10 11 or 18 or a krypton atom X double bond to X 310 X specifies that a double bond to X must exist Equivalent to writing X bond double X may be either an element symbol an id for another type specifier or a list containing one or both of these to allow more flexible specifications If used inside the bracketed part of a ring description this only indicates that the atom type should be present within the cycle the connection to the target atom is unimportant If used in a chain keyword the connection type is honoured Table 12 4 NETA X Keyword Examples Command Meaning 0 A double bond to an oxygen atom 04 A double bond to an atom which matches type ID 4 see Reusing Types in section 12 5 4 bond The bond keyword defines the specific type of the connection
207. lyphs Window TODO XXX Glyphs Window The glyphs window allows new glyphs to be created by hand or existing glyphs in the model to be managed edited and deleted Figure 5 13 Glyphs Window All glyphs in the current model are listed to the left Selecting one will allow its properties to be edited on the right The type of glyph can be changed also Colours for individual glyph data i e points may be changed through the colour controls associated to each 79 7 16 Grids Window The Grids window provides management for grid data sets owned by the different models All grid data sets held by the current model are displayed here The appearance of individual grids may be changed and axes cutoffs changed Grid data can also be cut copied and pasted to different models A grid in Aten s world can be more or less any kind of volumetric or surface data For instance orbital densities 2D height maps molecule probability densities etc See the Grids section for more information Grids o x File Edit Data Cutoff Origin Axes Style Shift lt gt Data Sums Minimum 0 0 Positive 0 0 Maximum 0 0 Negative 0 0 NPoints 0 Total 0 0 Cutoffs Primary Secondary Lower 0 00000000 0 00000000 Upper 0 00000000 O 0 00000000 0 View 0 0 0 0 Figure 7 23 Grids Window Data Cutoff page General Grid Management Each grid in the list has associated with it a checkbox that determines whether or not it is curr
208. m is using the target atom s bonds in order to identify it atoms to a depth of 1 bond are being used to describe the atom If these bound atoms are in turn described by their bound neighbours then atoms to a depth of two bonds are being used For example Table 12 1 NETA Descript Depth Examples Example Description Effective Depth nbonds 4 Zero contains specifications relevant to the root atom only nbonds 4 H C 1 root commands and first bound neighbours nbonds 4 H C H n 3 2 root commands first and second bound neighbours Any depth of description can be handled by Aten becoming as complex as is necessary to uniquely identify the target atom 12 5 3 Type Scores 307 In a forcefield with many defined types more than one type may match an atom in a molecule In order to best assign types to atoms Aten scores each type description according to the number of terms defined within it one point for each term satisfied Once a matching type for an atom is located in the forcefield it is assigned to that atom but the search for a better scoring type continues If a match with a higher score is found it replaces the previously assigned type If a match with the same score is found the previous type is not replaced Non Matching Types Score 1 When a type description is tested for a given atom it accumulates points for each term in the description that is satisfied by the environment of the atom As soon as
209. mmand The list of possible options is Option Effect solid Render the glyph in solid mode if the glyph supports it Same as calling glyphsolid TRUE after creation text string Set the character data associated to the glyph to string Valid only for glyphs which display text wire Render the glyph in wireframe mode if the glyph supports it Same as calling glyphsolid FALSE after creation For example newglyph cube creates a new cube in the model newglyph text text I am some textX 185 creates a new text glyph in the model reading I am some text Note the need to escape the quotes surrounding the text newglyph tetrahedron wire creates a new wireframe tetrahedron in the model 186 9 14 Grid Commands Add gridded data to the current model Grid window for management of grids in the GUI addgridpoint Syntax void addgridpoint int ix int iy int iz double value Set a specific data point in the current grid For example ercloloeaichoostiog 4 i Id 45 28 2 set the grid value at point 4 1 15 in the dataset to 4 123 addnextgridpoint Syntax void addnextgridpoint double value Add the next sequential grid point starting at 1 1 1 and proceeding through dimensions as defined by the gridlooporder command default is x gt y gt z i e 1 1 1 is set first then 2 1 1 3 1 1 etc For example addnextgridpoin
210. n please check the parameters in the file are what you actually want Aten is designed to ease the pain of setting up a simulation in this manner but is not intended as a black box 12 2 1 Canongia Lopes amp Padua Ionic Liquids cldp il ff All atom ionic liquids forcefield of Canongia Lopes et al covering various cation anion combinations References o J N Canongia Lopes A A H Padua J Phys Chem B 110 39 19586 19592 2006 o J N Canongia Lopes A A H Padua J Phys Chem B 108 43 16893 16898 2004 o J N Canongia Lopes J Deschamps A A H Padua J Phys Chem B 108 30 11250 2004 o J N Canongia Lopes J Deschamps A A H Padua J Phys Chem B 108 6 2038 2047 2004 290 12 2 2 Youngs Kohanoff amp Del P polo dmim Cl dmimcl fm ff Force matched model for the ionic liquid dimethylimidazolium chloride only Integer charges on ions References o T G A Youngs J Kohanoff and M G Del P polo J Phys Chem B 110 11 5697 5707 2006 12 2 3 Youngs amp Hardacre dmim Cl dmimcl fm2 ff Second force matched model for the ionic liquid dimethylimidazolium chloride only Non integer charges on ions References o T G A Youngs and C Hardacre ChemPhysChem 9 11 1548 1558 2008 12 2 4 Jorgensen at al OPLS AA oplsaa ff Original OPLS AA forcefield of Jorgensen et al Thanks to W Jorgensen for supplying the parameter data References o W L Jorgen
211. n p getpattern solid gets the pattern named solid in the current model setting its reference in the variable p getpattern 3 gets the third pattern in the current model listpatterns Syntax void listpatterns List the patterns in the current model For example listpatterns newpattern Syntax pattern newpattern string name int nmols int atomspermol 218 Add a new pattern node to the current model spanning nmols molecules of atomspermol atoms each and called name A reference to the new pattern is returned For example pattern p newpattern water 100 3 creates a new pattern description of 100 molecules of 3 atoms each named water i e 100 water molecules in the current model and returns its reference Methods of reading and writing data from to files in import and export filters Many commands here use formatting strings to provide formatted input and output All reading and writing commands here work on input or output files as defined internally by the program Messaging Commands for commands that write to the screen Formatting Output for more details on the C style formatting of data employed by some commands Delimited Reading and Writing for details on the parsing of delimited data as employed by some commands addreadoption Syntax void addreadoption string option Controls aspects of file reading See Parse Options for a list of poss
212. n turn bound to carbon atoms i e all hydroxyl hydrogens expand Syntax int expand Expand the current selection of atoms by selecting any atoms that are directly bound to an already selected atom The number of atoms added to the previous selection is returned For example expand invert Syntax int invert Inverts the selection of all atoms in the current model Returns the number of atoms selected For example ae 8 select Syntax int select atom int string selection Select atoms in the current model keeping any previous selection of atoms See the deselect command for a full description of the syntax The number of atoms added to the existing selection is returned For example select 5 selects the first five atoms ime n select Mes anne 232 selects the first five atoms and all hydrogens storing the number of new atoms selected in the variable n selectall Syntax int selectall Select all atoms in the current model The number of selected atoms is returned For example selectall selectfftype Syntax int selectfftype string fftype Select all atoms with forcefield type fftype in the current model The number of atoms selected is returned For example selecttype CT selects all atoms that have been assigned the forcefield type CT selectf Syntax int selectf string format Select
213. name alumina belongs to spacegroup C2 m number 12 Symmetry related copies of the five atoms present in the cell can then be generated Any overlapping atoms resulting from the application of the spacegroup s generators are automatically removed Y Build Open the Cell Define Window again and on the Spacegroup page enter the spacegroup as C2 m or 12 and press Set to assign the spacegroup to the model Then generate symmetry equivalent atoms by pressing the Pack button 24 A Aten vL7 r1671 Unnamed001 lt lt no filename gt gt Modified File Edit View Selection Model Trajectory Forcefield Settings Scripts Help DAR Se DA it weeosvsaeaRanwses Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click 20 Atoms 407 844000 g mol drag or rotate in local frame right click drag ctrl remove from selection Parallelepiped 3 603856 g cm Replicate Cell and Recalculate Bonds The basic crystal unit of 0 alumina isn t too interesting on its own so lets create a chunk to properly see the structure Replicate the unit cell by 3 or 4 units in each positive direction or more if you re feeling adventurous and then calculate the bonding in the model Y Build Open the Cell Transform Window and on the Replicate page set each positive replication direction to 3 or 4 Press the Replicate button to genera
214. ndered in addition to the components that make up a standard model i e atoms bonds and unit cell These can be used to illustrate points of interest in a system illustrate some vector quantity or draw whole new objects from scratch Glyphs can be drawn at fixed positions within a model or can have their vertices linked to existing atoms enabling them to be moved in conjunction with the model s atoms Some glyphs can also be rotated about their current position A glyph requires from one to four vertices to be set depending on the type A different colour may be assigned to each vertex enabling for example each corner of a triangle to possess a different colour The available glyph types and the roles of the four possible coordinates are Table 10 1 Glyph Types Glyph Rot rl r2 r3 r4 arrow No Tail coords Head coords cube Yes Centroid XYZ scaling factors ellipsoid ellipsoidxyz line No Start coords End coords quad No Vertex 1 Vertex 2 Vertex 3 Vertex 4 sphere Yes Centroid XYZ scaling factors svector No tetrahedron Yes Vertex 1 Vertex 2 Vertex 3 Vertex 4 text No Mid left anchor of text text3d No Mid left anchor of text triangle No Vertex 1 Vertex 2 Vertex 3 tubearrow No Tail coords Head coords vector No Centroid Pointing vector 263 10 3 Patterns Patterns in Aten represent collections of molecules of the same type and are used primarily in the forcefield engine where they allow the construction of compact descriptio
215. ndesirable or unintended then performing the scaling with no pattern definition will scale the position of each atom separately Cell Transform o x Replicate Scale Rotate Miller Rotate 90 around X Rotate 90 around Y Rotate 90 around Z cs Ul eee Figure 7 11 Cell Definition Window Rotate page Not currently implemented Cell Transform o x Replicate Scale Rotate Miller Indices h1 Sikio S Mo Direction MO In Lo Out Select Cut Figure 7 12 Cell Definition Window Miller page The Miller page allows the model to be cut so that various Miller surfaces are left behind The hkl indices of the desired Miller plane should be entered in the three spin boxes and the resulting plane s will be drawn onto the current model The deletion of atoms can be done in one of two ways removing either those atoms that are inside or those atoms that are outside of the defined Miller plane and its periodic or symmetric equivalent 66 7 10 Command Window The command window allows commands or sequences of commands to be run and stored for later use allows management and execution of scripts and provides access to searchable command help Command Console o x Prompt Interactive Scripts Command Help Y Force Update aten prefs usenicetext FALSE aten prefs usenicetext TRUE Figure 7 13 Command Window Prompt page Any command or compound command can be entered in the bottom e
216. nents selected in the previous window If a partition has been defined it is necessary to assign the components to a certain partition The components will be added to the whole cell if this is not the case There are various options available to set the desired population number and or density for each component The options are as follows The exact number required for each component may be specified The specific density of the component may be given The exact number of components may be requested and a density defined Disordered Builder Window Figure 5 9 Disordered Builder Window The list at the top of the panel gives all the currently loaded molecules that are suitable for use as components the main criterion is that they do not themselves possess a unit cell Next to the name of each model in the list is a number which specifies the number of molecules that you want to be inserted into the target model and two checkboxes that allow certain Monte Carlo move types to be prevented for individual molecules The first checkbox if unticked prevents rotations both on insertion and in standard Monte Carlo moves of the model while the second checkbox if unticked will prevent the standard Monte Carlo translation move from being used with this model If the number is set to zero the default for all components then no insertions of that model will be attempted The disordered builder needs a model with a cell already defined
217. ng E Current Energy Current Forces E Current Energy Current Forces Minimiser Minimiser Forcefield MOPAC Forcefield MOPAC Steepest Descent Simple v Method RHF AM MOZYME Convergence Criteria Spin Singlet v Energy 1 0E 5 Hamiltonian PM6 v RMS Force 1 0E 4 Q Charge 0 0 Max Cycles 100 Q Mini mise Q Mini mise Figure 7 17 Forcefields Window Energy minimisation controls Energy Minimisation The Energy page provides the means to perform geometry optimisations on loaded models using one of several methods The forcefield selected in the Forcefields page is used to perform the minimisation unless one has previously been explicitly associated to the model The current energy and forces may also be calculated akin to single point energy calculations The MOPAC minimiser requires that the locations of a valid MOPAC executable and temporary directory are defined see Section 14 2 for more information A job file is automatically written to disk and MOPAC executed when Minimise is clicked and the results loaded back in Output of the program is buffered to the Messages window see Section 7 17 Forcefield Management Forcefield files are managed through the Forcefields page A list of currently loaded forcefields is provided in the form of a drop down list at the top the selected item is the current default forcefield and is used whenever one is required by a process but none has been linked to the target model Th
218. ning that any number of tabs commas and spaces may separate items Text items should be enclosed with either double or single quotes if they themselves contain these delimiters in particular this applies to NETA descriptions There is no terminating symbol at the end of a line c f the command language where a typically ends every command The majority of data is contained within blocks in the file Blocks begin with a specific keyword e g inter contain one or more lines of definitions and are terminated by an end keyword Forcefield files may contain many blocks of the same type permitting terms of the same type but with differing functional forms to be defined easily More advanced forcefields may contain generator sections and functions that enable them to either generate all their parameters on the fly from a basic set of data or fill in missing terms that are not defined in any blocks 12 1 2 Example SPC Water The format is keyword based and as simple as possible Most input is enclosed within blocks beginning with a keyword and terminated after several lines of data with and end statement As an example of the overall structure of a forcefield consider the simple point charge SPC forcefield for water as is provided with Aten name SPC Water units kj types il HW H nbonds 1 2 OW O UA SEN 289 end above ALS 1 HW 0 41 ORO ORO 2 OW Omar 0 650 JLEG end bonds constraint HW OW ated OMe OO end
219. ns as used when combining similar Lennard Jones parameters Table 16 6 Combination rules arithmetic The arithmetic mean of two values a 0 5 b c geometric The geometric mean of two values a sqrt b c customl Custom combination rule custom2 Custom combination rule 327 custom3 Custom combination rule 16 7 Drawing Styles Available drawing styles for individual atoms are Table 16 7 Draw style keywords Value Description stick Atoms and connected bonds are drawn using simple lines tube Atoms and connected bonds are drawn using capped cylinders sphere Atoms and connected bonds are drawn using spheres and cylinders with all atoms the same size scaled Atoms and connected bonds are drawn using spheres and cylinders with all atoms sized according to their atomic radius set in the preferences 16 8 Energy Units A list of energy units supported by Aten Table 16 8 Energy unit keywords NENE Description Joule Equivalent j Joules per mole J mol 1 0 kj KiloJoules per mole kJ mol 1000 0 cal Calories per mole cal mol 4 184 kcal KiloCalories per mole kcal mol 4184 0 K Kelvin K 1 0 503 2166 4184 0 ev Electronvolts per mole e V mol 96485 14925 ha Hartrees per mole Ha mol 2625494 616 16 9 Glyph Types Available glyph types drawing objects are Table 16 9 Glyph type keywords Value Description arrow Simple arrow cube A cuboid ellipsoid An ellipsoid oriented by face and edge vector
220. ns of systems where many similar molecules exist e g liquids A set of patterns describing the contents of a model is often referred to as a pattern description Such a description is generated automatically as and when required by Aten and so in most cases should not need to be defined manually by the user When Aten fails to find a suitable pattern for a model this is often an indication that a bond is missing perhaps the bond tolerance is too low or the atoms present in the system are not in exactly the order you think they are When Aten fails to find a proper pattern definition for a system some operations will not be performed e g folding molecules back into the cell with Model Fold Molecules In these cases it is best to take a careful look at the ordering of atoms and their bonds within a system to try and fix the cause of the problem but a default pattern can be enforced if absolutely necessary through the main menu s Forcefield Add Default Pattern option This description adds in a simple pattern that encompasses all atoms in the model and therefore always succeeds at the expense of inefficiency A collection of atoms can live quite happily on its own in Aten and can be moved around rotated deleted and added to at will However if you want to calculate the energy or forces of a collection of atoms or employ methods that use such quantities then a description of the interactions between the atoms is required Creating a su
221. nstall somewhere other than the default location you ll need to tweak the PowerShell profile given in Step 7 2 3 5 Download GLext Header Go to http www opengl org registry api glext h and save the page as glext h somwhere like your My Documents directory Again if you choose somewhere other than this location you ll need to tweak the PowerShell profile given in Step 7 2 3 6 Download and Unpack Qt4 Source Go to http qt nokia com downloads and download the LGPL package for Windows approx 322 Mb and run the installer file Again you may choose where to unpack the files to the default is C Qt 2010 05 for the release downloaded here but if you change the default you ll need to modify the relevant paths accordingly in Step 7 You may choose not to install the MinGW part of the package since we will be using Visual Studio for the compilation There is no need to run Qt Creator once the installation is finished 2 3 7 Install and Setup Windows PowerShell Download PowerShell from http support microsoft com kb 968930 Once installed run PowerShell its Start Menu entry is typically placed inside the Accessories folder and you should be presented with a blue shell starting inside your Documents and Settings folder C Documents and Settings Your Name First thing is to set up your profile with the relevant paths set so we can find the Visual Studio readline and Qt4 files Such settings are stored
222. nt As an example consider the following definitions for trifluoroethanol from the OPLS AA forcefield where the environment for each atom is described in full for each type 308 160 161 IEZ 163 164 155 CT OH HO HC mymoaqa Walp late aoe F n 3 WE Cama O ae C F n C nh 2 o H H Cia pac ee E h 2 0 5 Pie Ga C nh ype Zo l GHZ ia SERE LOLOSE TINNA MEITSI LN Ca iE LUOTOT LN OH in trifluoroethanol HO in trifluoroethanol F in trifluoroethanol H in trifluoroethanol For each atom type the whole of the trifluoroethanol molecule is described but each type tends to share a common chunk of NETA definitions with the other types As an alternative then we can define one or two of the involved types explicitly as above and then specify the rest of the types relative to this one 160 161 EG 163 164 105 CT OH HO BC ao tra fae OOO YA ll O 5160 5160 OO EC GOO 5160 H C F n 3 CH2 in trifluoroethanol CF3 in trifluoroethanol OH in txtilucrocthanol HO in trifluoroethanol F in trifluoroethanol H in trifluoroethanol Much neater Or should that be not much NETA Hmmm Anyway reusing types in this way is a powerful way to reduce the complexity of type descriptions required for a given molecule or fragment Typically it is advisable to pick an atom that is fairly central to the mole
223. number of molecules of each and permits the typing routines to consider only one molecule of each species when determining atom types etc The assumption here is that 321 since all molecules in a given species will have the same chemical graph atom types can be worked out for a single molecule and then duplicated on all of the others Following detection of a suitable pattern description several tasks are then performed Cycle Detection Firstly any cyclic structures within a single molecule are detected up to a maximum adjustable ring size This is achieved from a series of simple recursive searches beginning from each atom with more than one bond A sequence of walks along bonds are made in order to form a path of some specified length i e ring size If the final atom in this path shares a bond with the starting atom a cycle has been found If not the final atom is removed and replaced with another If there are no more atoms to try in this final position the preceeding atom in the path is removed and replaced with another and so on Each unique ring its size and pointers to the sequence of constituent atoms is stored in the pattern Assignment of Atom Environment From the list of bound neighbours each atom is assigned a simple hybridicity based on the character of the bonds it is involved in mainly used for the determination of aromatic cycles in the next step Ring Types Once atom hybridicities have been assigned rin
224. ny subsequent script command or filter Note that declarations of variables with the same name made in scripts commands and filters will override any passed value names in order to avoid conflicts and breaking of existing filters and scripts The intended use is to be able to pass values easily from the command line into scripts or one line commands For example in a bash shell bob pe gt for num in 10 0 50 5 100 0 do aten double d num c printf Value age Sue e reptil O 9 come E export lt nickname gt Enter export mode where each model specified on the command line is loaded and saved in the format corresponding to the lt nickname gt specified If specified in conjunction with batch batch export mode is entered instead with commands run on models before being saved to the new format See Section 6 3 for details and a list of other modes exportmap lt name element gt Manually map assigned atom typenames in an expression to the names defined here when expressions are written to a file For example bob pc gt aten ff spc ff data test water xyz exportmap OW Ospc H Hspc c saveexpression dlpoly water FIELD quit 47 writes the water forcefield with the OW and HW atomtype names mapped to Ospc and Hspc respectively expression lt file gt Loads the specified file as if it were an expression F f lt nickname gt format lt nickname gt For any forthcoming mode
225. o 9 Atom Shift None Selection All Wa Nu Wa Figure 7 26 Grids Window Shift page The Shift page can be used to translate the grid data points along each axis of the data set allowing for instance isosurface features of interest in a periodic grid to be displayed in a more central position Note that no modification of the actual grid data is performed the effect is entirely visual The Atom Shift group allows translation of selected all atoms in the parent model to be moved at the same time so as to correlate them with the new positions of the grid data Orbitals Page Not implemented yet 82 7 17 Messages Window Messages Aten version 1 7 http aten googlecode com svn trunk 1603 built on Fri 01 Apr 17 13 Copyright C 2007 2011 T Youngs Aten uses Space Group Info c 1994 96 Ralf W Grosse Kunstleve Aten comes with ABSOLUTELY NO WARRANTY This is free software and you are welcome to redistribute it under certain conditions For more details read the GPL at lt http wwww gnu org copyleft gpl htmi gt Figure 7 27 Messages Window The messages window is simply that a place for all of Aten s text output to appear when the GUL is active 83 7 18 Position Window Tools for the absolute positioning of atoms are available here All work on the current selection of atoms in the current model Position o x Centre Flip Translate Shift Reposition Target Coordinates X 0 000000 9 1
226. o atoms or the whole model Select the relevant tool and simply click on atoms in the main view The element of new atoms when drawing atoms or chains as well as the transmutation target element is determined by the currently selected element button The bottom half provides tools to draw individual bonds between atoms or to calculate bonds automatically Drawing a bond requires pairs of atoms to be clicked sequentially once the tool is activated Build Tools o x Edit Tools Options Add Atom X 0 000001 Y 0 000000 Z 0 000000 gt Fractional Coords Add Figure 7 5 Build Window Tools page 62 The Add Atom tool allows atoms to be created at specific positions in the model Coordinates are entered and the atom created with element defined by the current selected element on the Edit page by pressing the Add button If the Fractional Coords checkbox is ticked the coordinates are assumed to be fractional and are converted to cell coordinates as the atom is added For example setting coordinates to 0 5 0 5 0 5 will create an atom in the centre of the current unit cell Build Tools o x Edit Tools Options Prevent Folding Figure 7 6 Build Window Options page Finally the Options page allows automatic folding of atoms to be restricted When transforming atoms in a periodic system with the mouse i e rotating or translating them if any move outside the unit cell as a result of the transformation they are automatically
227. o look for them Sometimes however you may need to tell Aten where these files are e g if you have not installed Aten after compiling the source yourself There are several ways of achieving this When running Aten from the command line the atendata switch can be used to specify the location of Aten s data files For instance bob pe gt aten atendata usr software aten data Alternatively the environment variable SATENDATA can be set For example in a bash style shell bob pc gt export ATENDATA usr software aten data In both cases Aten should be directed to the data directory either it s installed location or the directory in the top level of the source distribution The structure of the data directory is as follows data filters Contains stock filters for import and exporting data data fragments Fragment models for drawing modifying models data ff Forcefield files data fftesting Forcefields that are incomplete or have not been tested data partitions Partition data for the disorder builder data test Various test files models grids etc not installed 4 2 2 User Files Aten will search for additional filters fragments and forcefields in a specific location in the user s home directory On Linux and Mac OS X systems this directory is called aten while on Windows the directory should be called simply aten 1 e without the preceding dot Within this directory exists optionally further directo
228. odel Select a loaded model which already has a cell definition as the target for the disordered builder The model may have existing contents which will be preserved during the build An optional partitioning scheme may be applied _ Create New Model and Define Cell Anew mode will be created and used as the target for the disordered builder The unit cell will be defined in the next step and an optional partitioning scheme may be applied Create New Model and Generate Cell Anew mode will be created and used as the target for the disordered builder The Shape of the cell will be defined in the next step while the final size will depend on the specified contents No partitioning scheme other than none may be selected in this mode Back Next gt Cancel Step 1 is to select either an existing model which has a unit cell or choose to create a new one Since the water molecule is the only one loaded in this example the existing model option is grayed out in the graphic above When creating a new model there are two options for the generation of the unit cell either you can specify the cell lengths and angles explicitly to get exactly the cell you want or you can specify just the angles and relative lengths of the cell which will then be enlarged automatically to contain whatever you choose to put inside it For this example we will do the latter so select the last option and click Next Disorder Wizard Y UD Step 2
229. odel 1 m2 newmodel Test model 2 209 currentmodel m1 creates two models storing references to each and then re selects the first one and makes it the current target again deletemodel Syntax voiddeletemodel int id void deletemodel string name void deletemodel model m Deletes the current model if no argument is given or the supplied model firstmodel Syntax model firstmodel Makes the first loaded created model the current model and returns a reference to it For example firstmodel info Syntax void info Print out information on the current model and its atoms For example ao 0 A finalisemodel Syntax void finalisemodel Performs various internal tasks after a model has been fully created within a filter Should be called after all operations on each created model have finished 210 For example finalisemodel getmodel Syntax model getmodel int id model getmodel string name model getmodel model m Returns a reference to the requested model but unlike currentmodel does not make it the current model For example model alpha getmodel alpha2 grabs a reference to the model named alpha2 model m getmodel 5 gets a reference to the fifth loaded model lastmodel Syntax model lastmodel Makes the last loaded created model the current model and returns a
230. of benzen 12 atoms followed by newpattern benzene 100 12 50 molecules of diethyl ether 15 atoms n wpatcerm tether o OS Calculate bonds within individual benzene and ether molecules rebondpatterns rebondselection Syntax void rebondselection Calculate bonding between atoms in the current atom selection For example rebondselection 140 9 3 Building Commands Tools to build molecules from scratch or finalise unfinished models When creating atoms using the commands listed below if the coordinates of the new atom are not specified then it is placed at the current pen position In addition the reference frame of the pen position is represented as a set of three orthogonal vectors defining the pen s local coordinate system set initially to the Cartesian axes centred at an arbitrary origin the pen position Subsequent rotations operate on these coordinate axes Think of it as a 3D version of the old school turtle addhydrogen Syntax void addhydrogen void addhydrogen atomlint i Satisfy the valencies of all atoms in the current model by adding hydrogens to heavy atoms If an integer id or atom reference is provided as the argument then the addition of hydrogen is restricted to the specified atom For example addhydrogen add hydrogens to all atoms in the current model addhydrogen 10 add hydrogens to atom 10 only bohr Syntax v
231. of command line arguments and a list of all recognised arguments 6 1 Switch Order Two important things to consider Firstly short options e g b d etc may not be concatenated into one long specification of a short option i e bd they must be given separately as b d or they will not be recognised Secondly the order of the given switches is important since their meaning is applied or acted out immediately For example bob pec gt aten nobond testl xyz test2 xyz will load the models test1 xyz and test2 xyz preventing recalculation of bonds between atoms in both However bob pe gt aten testl xyz nobond test2 xyz will only prevent recalculation of bonds for the second model The reason for acting on switches and arguments in the order they are encountered on the command line is to allow for flexibility especially when using Aten as a non graphical processor Note The position of debug switches or those affecting the verbosity of the program has no bearing on the timeliness of their effect they are dealt with first by Aten regardless of where they appear in the program s arguments 6 2 Switches A atendata lt dir gt Tells Aten to use the specified dir as its data directory where filters etc are stored This overrides the ATENDATA shell variable B b bohr Specifies that the unit of length used in any models and grid data that follow is B
232. often stored in the same output file In this case the importmodel filter can detect the presence of the additional trajectory frames and manually attach them to the parent model The following sections explain the details of how both methods work 11 2 1 Trajectories in Separate Files DL_POLY being a molecular dynamics code stores its configuration and trajectory data in separate files Filters are supplied with Aten that read in DL_POLY trajectories and so this example will revolve around those filters Necessity for a Master Configuration Thus far it has been implicity stated that the master configuration and the trajectory files come necessarily as a pair the master configuration is read in and then the trajectory associated to it This implies that the trajectory file is somehow tied to the master configuration perhaps the trajectory file does not contain information such as the number of atoms or element data and so a reference configuration is necessary Of course this may not always be the case and it is possible that some trajectory formats will store all the necessary information needed in order to fully generate the trajectory configurations DL_POLY trajectories do in fact contain all the necessary data but even so the master configuration is still used as a template for the trajectory data and is used to check that the correct number of atoms are present etc It comes down to a matter of preference as to wheth
233. ohr rather than A and should be converted to the latter 45 batch Enter batch processing mode modifying and saving models to their original filenames See Section 6 3 for details and a list of other modes bond Force recalculation of bonding in loaded models regardless of whether the filter used any of the rebond commands see the list of bond related commands in Section 9 2 C c lt commands gt command lt commands gt Provides a command or compound command to execute Commands should be enclosed in single quotes to prevent the shell from misquoting any character strings and individual commands separated with semicolons Commands provided in this way can be used to set up Aten in the way you want it from the command line perform operations on model files before loading the GUI or perform operations on model files without loading the GUI at all For example to start the GUI with a new model named cube that has a cubic cell of 30 side length bob pc gt aten c newmodel cube cel1 30 30 30 90 90 90 Similarly to load a model and make a duplicate copy of the atoms pasted into the same model bob pc gt aten original xyz c selectall copy paste 10 10 10 In both cases the GUI initialises itself without being told but this can be prevented with the quit command Consider the last example to save the newly expanded model and quit without ever launching the GUI bob pc
234. oid bohr object x Converts the specified object s data to A assuming that it is currently specified in Bohr For example atom i aten model atoms 2 bohr i converts the coordinates of the supplied atom from Bohr to A 141 chain Syntax atom chain int string el atom chain int string el int string bondtype atom chain int string el double x double y double z atom chain int string el double x double y double z int string bondtype Create a new atom of element e1 at the current pen position or the specified coordinates bound to the last drawn atom with a single bond or of type bondt ype if it was specified The element can be provided as a character string containing the element symbol or element name instead of the integer atomic number A reference to the new atom is returned For example APONTE places a carbon atom at the current pen coordinates and creates a single bond with the last drawn atom atom i chain 8 double places an oxygen atom at the current pen coordinates and creates a double bond with the last drawn atom com a Cama cane 4 0 3 0 Gad simone creates a chlorine at coordinates 4 0 5 0 6 0 joined by a single bond to the last drawn atom endchain Syntax void endchain Ends the current chain so that the next atom drawn with chain will be unbound For example endchain
235. oid setrx double d int id Set the x coordinate of the current or specified atom 134 setry Syntax void setry doubl e d void setry double d int id Set the y coordinate of the current or specified atom setrz Syntax void setrz double d void setrz double d int id Set the z coordinate of the current or specified atom setvelocities Syntax void setvelocities void setvelocities double vx double vx doub le vy doub le vy doub Le VZ doub V int id Set the velocity components of the current or specified atom setvx Syntax void setvx doubl e d void setvx double d int id Set the x velocity of the current or specified atom setvy Syntax void setvy doubl e d void setvy double d int id Set the y velocity of the current or specified atom setvz 135 Syntax void setvz double d void setvz double d int id Set the z velocity of the current or specified atom show Syntax void show atom int id 0 Makes the current selection of atoms or the supplied atom visible again if they were previously hidden 136 9 2 Bond Commands Create bonds and perform automatic bonding operations augment Syntax void augment Augments bonds in the current model automatically de
236. ol created unless the newline command is given Then the control will be added at the beginning of a new row A group box or tab control takes up a single column by default The parentspan property can be set to override this at the time of creation of the group tab control For example adding parentspan 2 to the list of arguments will force the group box or tab widget to span two columns instead of one All controls take up a single column by default The span property can be set to override this For example adding span 5 to the list of arguments will force the control to span five columns instead of one The associated label will still use only one column unless this is overridden by the 1abelspan property Some control over the states content of other controls is possible using the state command The value part indicates when the change detailed in action is performed on the control name Since a direct equality comparison between the current value of the control and the state change value is made only integer and string values make sense here The control name is the target control for the specified action where action is one of checked disable enable items minimum maximum originalitems step or value For those actions that take a property value e g checked the format of the line is then value Oname action pr
237. om IDs involved in the interaction termid int Array index of forcefield term in relevant list ffangles ffbonds or fftorsions in local pattern type string Returns the Bound Type Section 16 3 of the interaction typenames stringl Array of typenames involved in the interaction vscale double Short range 1 4 scaling factor for torsion interactions 8 2 13 Bound Type Functions parameter Syntax double parameter string keyword Search for and return the named parameter of the bound interaction 8 2 14 ColourScale Type The colourscale type allows direct access to the points defined inside a colourscale Table 8 8 ColourScale Type Members Member Type RW Description npoints int Number of points contained in the colourscale points colourscalepoint Array of points in the colourscale 8 2 15 ColourScale Type Functions addpoint Syntax 104 colourscalepoint addpoint double value double r double g double b double a 1 0 Add a new point to the colourscale at point value and RGB A colour specified the components of which should have values ranging from 0 0 to 1 0 inclusive clear Syntax void clear Clear all points contained in the colourscale colour Syntax void colour double value double amp r double amp g double amp b double amp a Retrieve the colour components for the value specified The RGBA values of the colour will be placed in the supplied variable
238. oms aten model natoms printf Number of frames is i n nframes for model f aten model frames f f for int n 1 n lt natoms n xyz n f atoms n r for int n 1 n lt natoms n xyz n xyz n nframes model f aten model frames newmodel Average for int n 1 n lt natoms n newatom f atoms n z xyz n x xyz n y xyz n z Copy and save this to a file named avgeom txt To run the example aten zmap singlealpha data test water66 spcfw CONFIG t data test water66 spcfw HISu s avgeom txt 38 5 7 Self Contained Liquid Chloroform Builder Script This script installed in the SATENDATA scripts directory is an example of a completely self contained script depending on no external model or forcefield files The chloroform model is built by hand and the necessary forcefield is constructed in the script itself before being used to create a box of liquid chloroform Only the density of the liquid and the desired number of molecules are required in order to build the system since the molecular volume is worked out from the density and the mass Build chloroform system First create chloroform model by transmuting a methane molecul Since C Cl distances will then be too short we lengthen them afterwards newmodel chloroform newatom C a ae select ion e 1E CO NTE SO Se CoS cance mn Set number of molecules and density
239. oms and angles in degrees on the Define View ABC page and then pressing the Define button Cell Definition o x Y Has Cell Matrix Define View ABC Spacegroup Spacegroup Naneo Remove Set Pack Volume 1000 000 A Figure 7 8 Cell Definition Window Spacegroup page The spacegroup assigned to the current model can be changed and removed on the Spacegroup page On its own an assigned spacegroup is just a number no modifications to the atoms are made by changing the assigned spacegroup Packing of atoms however is a different matter Once a spacegroup is assigned symmetry equivalent atoms may be generated by use of the Pack button This assumes that the current contents of the model represents the symmetry unique set of atoms i e the minimal generator set which along with the spacegroup and unit cell defines the entire crystal 64 7 9 Cell Transform Window Transformations of the unit cell and its contents can be made here encompassing geometric scaling of the cell and atoms contained within and replication of the system in three dimensions Cell Transform o x Replicate Scale Rotate Miller 0 00000 gt X 1 00000 0 00000 Y 1 00000 0 00000 Z 1 00000 9 vV Fold Before Y Trim After Replicate Figure 7 9 Cell Transform Window Replicate page The Replicate page allows the current cell to be replicated along its three principal axes in both positive and negative directions The six inputs re
240. oms is similar 10 OH O Maly E Aly R Y Alcoholic O Li O cbx O GOGO Jal Carboxylic acid O 12 OH_cbx O H C O bond double Carboxylic acid O H Of course we could just have specified nbonds 1 for the doubly bound oxygen of the carboxylic acid group but this hides information as to the true connectivity of the atom 306 Example 3 N N 2 5 tetramethylpyridin 4 amine N At last a proper problem an asymmetric substituted pyridine Lets assume that we need to distinguish between every non hydrogen atom we ll skip describing the hydrogen atoms for now but note that this is most easily achieved by specifying directly the atomtype that the H is bound to see later on Let s start with the pyridine nitrogen We basically need to say that its in a 6 membered aromatic ring L3 N py N ring size 6 aromatic Pyridine N TODO 12 5 2 Description Depth Many subtleties related to the form of type descriptions are perhaps evident from the examples given above It is useful to think of type descriptions as having many different depths loosely corresponding to the number of bonds followed away from a central atom the target atom or the one currently being tested against the type description The target atom of the type description is the root of the description since all connections are defined relative to this atom A type description requiring specific connections to this target ato
241. operty Similar to the group command this adds the widget to an existing page in an existing tab widget or creates one or both and adds it there For example to add a control to a page named Extra in a tab widget called My Tabs you can specify tab Extra My Tabs as an argument 277 278 11 2 Trajectory Files Trajectory files usually mean one of two things either a sequence of frames from a molecular dynamics simulation trajectory or a sequence of configurations from a geometry optimisation of some kind Either way both boil down to the same thing from Aten s perspective that is a set of models in a sequence In terms of displaying such a set of models either they may be loaded as individual models i e having a separate tab in the GUD or the sequence of models may be associated to a single parent model Most commonly the latter is the preferred method especially when large numbers of models are present in the trajectory There are two related ways to get this data into Aten From the perspective of molecular dynamics simulations the parent model or configuration and the trajectory frames are stored in separate files In this case the model can be loaded first and then the trajectory file attached or associated to this model afterwards From the perspective of geometry optimisations for example the parent configuration 1 e the starting point of the optimisation and the sequence of coordinates are most
242. or double phi 180 0 phi lt 180 0 phi 5 settorsion 2 1 4 6 phi omie WEA oie LL ile CE la tone Vol omin eycevalainoyeleul ieronerssal toavevoueuarony 0 y aten model vdwenergy aten model elecenergy quit Note that the use of the q option means that only fundamental error messages and user output through the printf statements in the command is printed all of Aten s other working information is suppressed 41 5 10 Running a Script on Many Models CLI Batch no aten c loadscript test script ascript keepnames gro batch c runscript ascript 42 5 11 Saving GAMESS US Input with Options CLD src aten src aten chloroprene 1 xyz chloroprene 2 xyz piperidine 1 xyz piperidine 2 xyz piperidine capped cr xyz export gamusinp dfttyp B3LY P basis_gbasis MCP DZP statpt_nstep 200 batch c mopacminimise 43 5 12 Printing all Bond Distances in a Model CLI aten data test methanol inp c for bond b aten model bonds b b printf Geometry f n geometry b 1 b j 44 6 Command Line Usage From a shell running Aten with no arguments will start up the code in GUI If model files are provided on the command line these will be loaded in so that when the GUI starts they may be hacked apart according to your desired tastes The command line is also a powerful way of editing without using the GUI at all What follows is a description of the usage
243. otal bond order for each particular element ranging from zero meaning natural or no penalty to some positive number The higher the positive number the more unhappy the element is with this number of bonds For example hydrogen atoms score 0 for a total bond order of 1 a small positive number 2 for 322 no bonds hydrogen ion and a very large positive value here 32 for any other bond order In this way we penalise the total bond orders that an atom does not naturally take on and always tend towards the lowest score i e the natural total bond order wherever possible When modifying the bond order of a particular connection the total bond order scores of both atoms are calculated once for the current connection and again for the potential new bond order of the connection If the new score is lower the change of bond order is accepted Pattern Detection As with many other routines in Aten a suitable pattern description is first detected for the system in order to isolate individual molecular species and make the algorithm as efficient as possible Augmentation of Terminal Bonds Bonds that involve a heavy i e non hydrogen atom connected to no other atoms e g C O in a ketone are treated before all others The bond order is modified such that the total bond order score for both atoms is as low as possible Augmentation of Other Bonds Following optimisation of terminal bonds all other bonds are modified us
244. oty Syntax void roty double angle Rotates the reference coordinate system about the y axis by angle degrees For example 145 oie Aor 0 4 rotates around the y axis by 45 degrees rotz Syntax void rotz double angle Rotates the reference coordinate system about the z axis by angle degrees For example cojea LOS 5 9 rotates around the z axis by 109 5 degrees selectionaddhydrogen Syntax void selectionaddhydrogen Adds hydrogen atoms to the current atom selection only shiftdown Syntax void shiftdown void shiftdown int n Move the current atom selection one or n places down in the atom list i e towards higher IDs For example shiftdown 4 moves the current atom selection down four places shiftup Syntax void shiftup 146 void shiftup int n Move the current atom selection one or n places up in the atom list i e towards lower IDs For example SHE CUPIO moves the current atom selection up one place transmute Syntax void transmute int string el Transmute the current atom selection to the specified element For example transmute EF changes all atoms in the current selection to fluorine transmute C1 changes all atoms in the current selection to chlorine transmute 6 changes all atoms in the current selection to carbon 147 9 4 Cell Commands Create remove modify
245. pack and replicate the model s unit cell adjustcell Syntax void adjustcell string parameter double value Adjust a single unit cell parameter one of a b c alpha beta gamma or one of the matrix elements ax ay az cz by the given value This does not set the specified parameter to the given value instead the supplied value is added to the existing value of the parameter For example evel Usiceculil Malo 0 increases the cell angle alpha by 5 degrees cn uste Yel T decreases the cell length c by 10 cell Syntax void cell double a double b double c double alpha double beta double gamma Set cell lengths and angles of current model This command will modify an existing cell or add a new cell to a model currently without a unit cell specification For example cell 20 07 1060 103 0 90 07 20 0 300 5 sets the model s cell to be orthorhombic with side lengths 20x10x10 cellaxes Syntax void cellaxes double ax double ay double az double bx double by double bz double cx double cy double cz 148 Set cell axes of current model This command will modify an existing cell or add a new cell to a model currently without a unit cell specification For example collares is 0 0 O ls OF O Op 1D sets the model s cell to be cubic with side length 15 A fold Syntax void fold Fold all atoms so they are within the boundaries of th
246. path Senv QTDIR Senv PATH Senv QTDIR qt bin Senv INCLUDE Senv QTDIR t qt include Senv LIB Senv QTDIR qt lib Dy Setup GnuWin32 environment variables Senv INCLUDE C Program Files GnuWin32 include Senv LIB C Program Files GnuWin32 lib Senv PATH C Program Files GnuWin32 bin Setup custom library and header environment variables Senv INCLUDE SHOME My Documents By default the running of scripts in PowerShell is likely to be disabled meaning that the profile will not be loaded when PowerShell next starts up To enable the execution of scripts run the following command PS C Documents and Settings Your Name gt set executionpolicy remotesigned You need to answer Yes to the question which then pops up Afterwards close this shell by typing PS C Documents and Settings Your Name gt exit and then restart PowerShell Y our new profile should now be loaded and you should see the Setting local environment message which we added to it All being well there should be no error messages here if there are then its likely that there s a mistake in one of the paths set in the profile 2 3 8 Build Qt4 First stage is to configure Qt ready for building by running the following commands PS C Documents and Settings Your Name gt cd C 0t 2010 05 qt PS C qt 2010 05 qt gt configure release opensource platform win32 msvc2010 eel
247. pes Syntax uatypes typeid typename element mass NETA description end The uatypes section contains exactly the same information as the types block except that a mass must also be provided In the types block it is assumed that the character element of the type also implicitly defines the mass as would be expected In the case of united atom forcefields this is not necessarily the case Thus the uatypes block allows a mass to be associated in order to account for the light atoms subsumed into the heavy atom s mass This information can be accesses through the mass member of the ffatom variable type For example vAtypes 10 CH2 cC 14 0265 nbonds 2 nh 0 United atom methylene carbon end describes a united atom methylene carbon with mass of 14 0265 C 2H ureybradleys 300 Syntax ureybradleys form XXXX end 12 3 3 Wildcards In any of the typenames given in the specification of intramolecular interactions a wildcard character may be used to finish off any or all of the typenames or replace individual typenames entirely In doing so a single definition is able to match more than one set of typenames For example bonds harmonic CN Els 4184 0 LOG end will describe bonds between CT and any other atom beginning with an H Using a on its own will match any typename in that position As an extreme example angles harmonic 5 ES a 418 4 109 4 end will match any angle Be caref
248. ple the ff style is particularly useful when loading in coordinate files which contain forcefield atom type names that do not always correspond trivially to element information e g DL_POLY configurations For example 273 zmap numeric indicates that atomic numbers are provided in place of element names and no conversion should be performed See Table 16 16 for a list of available z mapping methods 11 1 5 Filter Options When writing data in many cases all the information that the filter wants to write is contained within the current model for example when outputting simple file formats such as xyz or Aten s own akf format In other cases ther may be additional data for which would be nice to have some control over and which lays beyond atoms and bondes The best example is probably the input formats for nearly all ab initio codes which contain as well as the atomic coordinates statements and additional data necessary to control the running of the code itself It is not a problem to write out static lines of control commands from the output filter but it would of course also be nice to be able to tailor this output from within the GUI or from the command line This can be achieved by assigning values to variables in the filter through the use of filter options Any number of options can be defined and some relatively simple but useful control over the layout of the related GUI controls is possible Defining Options A f
249. pper primary cutoff value visible int Flag specifying whether the grid is visible i e should be drawn in the model 8 2 30 Measurement Type The measurement type stores the atom indexes and current value of a single measurement currently displayed on a model Table 8 19 Measurement Type Members Member Type RW Description atoms atom Array of atoms involved in the measurement 1 atom First atom involved in the measurement atom Second atom involved in the measurement k atom Third atom involved in the measurement if any l atom Fourth atom involved in the measurement if any literal double The literal value e g distance angle or torsion angle of the measurement using atom coordinates as is without applying minimum image criteria in periodic systems value double Value e g distance angle or torsion angle of the measurement 8 2 31 Model Type The mode1 type contains all the information describing a single model within Aten including bonds grid data measurements etc Table 8 20 Model Type Members Member Type RW Description angles measurement List of current angle measurements in the model atoms atom Array of atoms in the model bonds bond Array of bonds defined in the model cell unitcell The model s unit cell componentbulk int Whether the component is to be considered a bulk component componentdensity double Requested density of the model componentfree int Whether the model or no
250. present negative and positive replication values for each direction most of the time its probably only useful to consider the positive right most replication directions Note that the numbers define the additional cells that will be created in addition to the original one So if all numbers are left at zero the original cell will remain untouched Entering a value of 1 for each positive direction will give a 2x2x2 supercell of the original cell and so on The representative unit cells of replicated and partially replicated copies of the current cell are drawn onto the current model Atoms in the model are folded into the unit cell prior to replication unless the Fold Atoms checkbox is unticked Similarly atoms that exist outside of the cell after replication are trimmed unless the Trim Atoms checkbox is unchecked Cell Transform o x Replicate Scale Rotate Miller X 1 00000 Y 1 00000 lt gt lt gt lt gt Z 1 00000 __ Scale Molecule COG __ Calculate Energy Change Scale Figure 7 10 Cell Transform Window Scale page The Scale page allows the principal axes of the current unit cell to be arbitrarily scaled along with the cell s contents If a valid pattern description exists for the model then the positions of individual molecules or bound fragments within the cell are scaled relative to their centres of geometry all intramolecular distances within molecules remains the same as before the 65 scaling If this is u
251. r filter will be loaded ready for use just as the normal stock of filters are The entire new filter file looks like this Bohr XYZ coordinates files for vl1 2 Created 19 07 2011 Last modified 19 07 2011 ChangeLog filter type importmodel name XMol XYZ Coordinates in Bohr nickname xyzb extension xyzb glob xyzb id 30 Variable declaration 36 filter type exportmodel name XMol XYZ Coordinates int natoms n m string e title doubl enr 12 1872 gt 0 8 econ EA Read data while eof readline natoms getline title newmodel title for n 1 n lt natoms n readline e rx ry rz q i newatom e I 6 rebond finalisemodel rx 0 529 ry 0 529 extension xyzb glob xyzb nickname xyzb id 30 y Variable declaration model m aten frame writeline m natoms writeline m name for atom i m atoms i 0 i writelinef 8s PLD GENOE AS yO CA O x BDO shiny O yODS at ZA DIO ZO C S 37 22 0320 2 a 6 EXE ols ai I2 6f TAL OE edb one 5 6 Calculate Average Coordinates CLI This example takes the supplied water trajectory and determines the average coordinates of all the individual water molecules Note that no accounting for the periodicity of the system is taken into account vector xyz aten model natoms int nframes aten model nframes int nat
252. r example cutis delete Syntax void delete Delete the current atom selection For example delete paste Syntax void paste 159 Paste the copied atom selection For example paste redo Syntax void redo Redo the last undone operation For example redo undo Syntax void undo Undo the last operation For example undo 160 9 9 Energy Commands Calculate energies for models and trajectory frames All printing commands refer to the last energy calculated for either the model or a trajectory frame ecut Syntax double ecut double ecut double cutoff Return or set and return the cutoff radius used in calculation of the electrostatics for a system For example ecut 15 0 sets the electrostatic cutoff radius to 15 0 A elec Syntax void elec string type none void elec coulomb void elec ewald double alpha int kx int ky int kz void elec ewaldauto double precision Set the style of electrostatic energy calculation to use either no electrostatics coulombic non periodic electrostatics or Ewald based electrostatics For the latter either the various parameters may be defined explicitly when ewald is the chosen method or may be estimated for the current system by using ewaldauto frameenergy Syntax double frameenergy Calculate en
253. r example gridstyle triangles 191 draws the current grid as a triangle mesh gridusez Syntax int gridusez int gridusez bool usez For two dimensional grid i e surface data this option controls whether the data value is used as the height z component of the surface or if no data value is used and the surface is flat If called with no arguments the current status of the option is returned 0 being off and 1 being on For example gridusez on gridvisible Syntax int gridvisible int gridvisible bool visible Set the visibility of the current grid i e whether it is drawn on screen For example gridvisible FALSE gridsize Syntax void gridsize string type int nx int ny int nz Initialises the current grid to be of the specified grid type and with the dimensions specified if the type requires it This must be called before any calls to addpoint or addnextgridpoint are issued For example gridsize regularxyz 64 128 64 192 initialises the current grid to be a regularly spaced and hold a total of gets calculator 524 288 points loadgrid Syntax grid loadgrid string filename Load an existing grid from the specified file and add it to the current model If successfully loaded a reference to the new grid is returned For example grid density loadgrid density pdens loads a grid called densit
254. rators in a rhombohedral basis Whether to frame the current model with a box Whether to frame the entire view with a globeaxescolour globecolour globesize glyphcolour hdistance imagequality keyaction labelsize levelofdetailstartz levelofdetailwidth levelsofdetail linealiasing manualswapbuffers maxrings maxringsize maxundo modelupdate mopacexe mouseaction mousemovefilter multisampling noqtsettings perspective perspectivefov polygonaliasing renderstyle quality double 4 double 4 int double 4 double int string 3 amt double double int string string 4 int int int int double int string int 126 box Colour of axis pointers on the rotation globe Colour of the actual rotation globe Size in pixels of the rotation globe in the lower right hand corner of the screen Default colour of all created glyphs Default H X bond distance to use when adding hydrogen atoms The general rendering quality i e number of triangles used to generate primitive objects of the images used if reusequality is set to FALSE otherwise the current quality value is used Current actions of the modifier keys Shift Ctrl and Alt Font pointsize for label text Z depth in Angstroms at which level of detail algorithm begins Z width in Angstroms of each level of detail strip Number of levels of detail to employ Enables disables line aliasing
255. readvarf data 3s 3s 4i 4 8 a b i d printf a s b s d f i i n i n a b d 1 n outputs 225 a abc b def d 56 000000 i 1234 n 4 The supplied format string contains a single space in between the two 3s specifiers and is significant since it corresponds to actual discarded space when processing the format Furthermore the last specifier 8 discard 8 characters is not fulfilled by the data string and so the number of arguments successfully parsed is 4 not 5 removereadoption Syntax void removereadoption string option Removes a previously set read option See Parse Options for a list of possible options For example removereadoption skipblanks rewind Syntax void rewind Rewind the input file to the beginning of the file For example rewind skipchars Syntax void skipchars int n Skips the next n characters in the input file For example Sietpehiaesuplionr discards the next 15 characters from the input file skipline 226 Syntax void skipline int n 1 Skips the next line in the file or the next n lines if a number supplied For example skipline skips the next line in the file skipline 5 discards 5 lines from the file writeline Syntax void writeline int double string var Write a line to the current output file that consists of the whitespace delimited contents of the
256. reference to it For example model final lastmodel listmodels Syntax void listmodels Lists all models currently available For example 211 listmodels loadmodel Syntax model loadmodel string filename model loadmodel string filename string filter lt automatic gt Load model s from the filename provided autodetecting the format of the file If the optional filter argument is present then the file is forcibly loaded using the filter with the corresponding nickname The last loaded model becomes the current model to which a reference is returned For example model m loadmodel home foo coords test xyz loads a model called test xyz returning a reference to it model m loadmodel home foo coords testfile xyz forces loading of the model test file as an xyz file modeltemplate Syntax void modeltemplate Can only be run when importing trajectory frames Templates the atoms in the trajectory s parent model by creating an equal number of atoms in the target trajectory frame and copying the element and style data Positions forces and velocities are not copied from the parent model atoms For example modeltemplate newmodel Syntax model newmodel string name 212 Create a new model called name which becomes the current model and return a reference to it For example newmodel emptymodel creates a ne
257. ries named similarly to those in the data directory in which user files of the relevant type should be located Finally the two main preferences files are located in the user s aten or aten directory Both are optional The first prefs dat or alternatively prefs txt is written by Aten from the Prefs window While this file may be modified by hand changes will be lost if overwritten by Aten The second file user dat or alternatively user txt is maintained entirely by the user and should be used to change or set up exotic situations and preferences For instance a specific forcefield could be loaded automatically on startup 16 4 3 Referencing Aten Aten has been published in the Journal of Computational Chemistry and the article can be found online here The full reference is Aten An application for the creation editing and visualization of coordinates for glasses liquids crystals and molecules T G A Youngs J Comp Chem 31 639 648 2010 It is not a requirement to cite Aten in your work but if you feel that Aten has been particularly useful then the credit would be nice 17 5 Usage Examples 5 1 Creating a Bulk Water Model GUI Bulk periodic systems are the staple diet of the molecular dynamicist particularly systems that are isotropic This example illustrates how to generate a simple bulk configuration of liquid water Make a Water Molecule We need a water molecule We could loa
258. rs are relevant Note that typenames given for a bond i j will also match a bond j i Data parameters should be provided in the required order for the specified form For example bonds constraint EEC AOOO 0 TOE end provides parameters for an H C bond using the constraint potential data Syntax data type name typeid typename datal data2 end The data block defines additional generic data for each atom type The additional data can be accessed through the datad datai and datas members of the f fatom type The quoted argument supplied to the block defines the data types and names to be expected for each specified atom type and furthermore stricly defines the order in which they must be given Any of the standard simple variable types int double and string may be used 295 Following the identifying typeid and typename data items are given one after the other and in the order they are declared in the block keyword argument For example data string dogtype int bridge int likespasta double numtoes 1 OW redsetter ii 0 9 2 HW dalmation il 1 64 end This defines a quartet of extra data albeit random odd data for each of the specified atom types For forcefields which rely on functions to generate the necessary function data the data block should be used to define additional data for each atom type For example the GAFF forcefield is able to generate extra intramolecular terms if the rel
259. rtp no yes al version Gromacs TOP file top top 14 no yes 2 Installation 2 1 From Precompiled Packages All Platforms The easiest way to get Aten is of course to download a precompiled installer for your system Installers are available for Windows Mac OS X and many Linux distributions through the website http www projectaten net and the OpenSuSE Build Service http download opensuse org repositories home trisyoungs 2 2 From Source Linux Mac OS X If you want to compile Aten by hand e g if you re keeping your own copy of the source and updating it via subversion then these guides may help They are very general and unavoidably quickly go out of date but they should provide some info to at least get started The Windows method is entirely different and somewhat more complicated than for Linux and Mac OS X but a working approach is documented here 2 2 1 Obtaining the Source From the Website as an Archive Go to http www projectaten net and grab the tar gz of the version you want and unpack it with bob pe gt tar zxvf aten 1 7 tar gz A directory called aten nn mm will be created containing all the guts of the code ready to build where nn mm is the current version number From GoogleCode with subversion If you want to build Aten from source and maintain a local copy so you can update it quickly to make the most of bugfixes and new features this is the best way of doing it You ll n
260. s ellipsoidxyz An ellipsoid oriented by an explicit set of provided axes 328 line quad sphere svector tetrahedron text text3d triangle tubearrow vector 16 10 A line between two points A quad made up of two triangles A sphere or spheroid A sense vector Regular tetrahedron Text rendered at 2D screen coordinates Text rendered at 3D model coordinates Regular triangle A fully 3D arrow An arrow centred on a point and pointing along a specified local vector Grid Styles Available drawing styles for surface grid data 16 11 Available grid Table 16 10 Grid style keywords Value Description grid All data points are drawn as simple dots at their coordinate positions the cutoff value is ignored points Data points above the cutoff are drawn as simple dots at their coordinate positions triangles A triangulated wireframe isosurface is drawn between points above the cutoff value solid A trangulated solid isosurface is drawn between points above the cutoff value Grid Types types Table 16 11 Grid type keywords Value Description regularxy regularxyz freexyz 16 12 Two dimensional surface data on a regularly spaced XY grid The grid size must be specified on creation with the gridsize command Three dimensional volumetric data on a regularly spaced XYZ grid The grid size must be specified on creation with the gridsize command Three dimensional data not restricted
261. s 8 2 16 ColourScalePoint Type The colourscalepoint is a simple type which allows definition of the point colour Table 8 9 ColourScalePoint Type Members Member Type RW Description colour double 4 Colour associated to the point 8 2 17 Eigenvector Type The eigenvector type stores the coefficients of a complete molecular orbital for a specific model Table 8 10 Eigenvector Type Members Member Type RW Description eigenvalue double Associated eigenvalue of the eigenvector name string Name of the eigenvector e g orbital symmetry occupancy double Associated occupancy of the eigenvector size int Current size of the eigenvector array Can be set to reinitialise the array vector double e The eigenvector data array 105 8 2 18 Element Type The element type stores all information describing a given chemical element the full array of which is stored in the aten type Table 8 11 Element Type Members Member Type RW Description ambient double 4 Ambient colour of the element colour double 4 Returns the ambient colour of the element Set this property to define both ambient supplied values and diffuse 0 75 supplied values components simultaneously diffuse double 4 Diffuse colour of the element mass double Atomic mass of the element name string Capitalised name of the element radius double Atomic radius of the element Affects the scaled sphere rendering style and bond calcul
262. s genuinely conceived without prior knowledge of that system NETA tries to keep the language simple enough that it can almost be read aloud an make sense given one or two special syntactic tokens rather than needlessly use numerical codes and spurious symbols to signify certain quantities or create an ultra compact language The former destroys readability and the latter promotes convolution neither of which help when trying to interpret old rules or write new ones So for the most part NETA is keyword based with a limited number of fairly natural symbols employed to denote common terms Typing begins from a provided set of atoms and bonds i e the chemical graph The connectivity between atoms must be set prior to typing either by automatic calculation of bonds based on distance criteria manually adding them by hand or reading them from the input model file The typing algorithm itself makes no additions or changes to the connectivity of the input structure NETA requires a knowledge of species molecule types in the model is required For single molecule systems there is 1 distinct molecule species and 1 occurrence of it For condensed phases e g liquids there are 1 or more species each with many copies of the molecule In the interests of efficiency for the following routines Aten attempts to generate a valid pattern description of the system if one is not present already This essentially picks out the individual species and the
263. s read all frames along the way and store file offsets for all frames Then seeking to any individual frame is a much quicker process Although style and editing changes are forgotten between frames the overall camera view of the model is linked to that of the master configuration and so is retained between frames If the trajectory cannot be cached and you require changes edits or styles to be made to each frame e g for the purposes of making a movie of the trajectory then a script is the way to go load frame apply edits save image etc Cached Frames If the trajectory is small enough to be stored in memory Aten reads in all frames at once This means that e Memory use is increased e Performance is optimal speed of moving between frames is fast because all frames are in memory e Edits are retained edits can be made to individual frames and will be remembered on moving to a different frame The size of the cache can be adjusted either from the command line with the cachelimit switch or by setting the cache limit member of the prefs variable within aten No check is made of the new cache limit with respect to the memory available on the machine on which Aten is running so use with care 281 In the current versions of Aten the total trajectory size is determined from the size of the frame on disk whereas it would be more appropriate to use the size of the frame in memory This will change in a future release 282
264. s are either selected automatically based on the filename extension or contents or picked by matching 267 only the associated nickname In the former case the first filter that matches the extension is used 11 1 2 Filter Locations A basic stock of filters is provided with Aten and installed with the program several default locations are searched for these filters on startup Alternatively if Aten fails to find these filters or you wish to point it to a suitable directory by hand either the SATENDATA environment variable may be set to the relevant path on Windows this variable is set by the installer or the atendata command line option may be used to provide the path Additional filters may be placed in a user s aten directory e g bob aten filters 11 1 3 Overriding Existing Filters Filters that possess the same ID or nickname as other filters of the same type may be loaded simultaneously with the last to be loaded taking preference over the other Thus an importmodel filter nicknamed xyz from Aten s installed filter stock will be overridden by one of the same nickname present in a user s aten filters or aten filters on Windows directory Similarly both these filters will be overridden by one of the same nickname loaded by hand from the command line with the ilter switch Note that this only holds true for filters referenced by nickname or determined automatically by Aten when loading data from th
265. s atoms according to a string generated from a C style printf call See the deselectf command for a full description selectfor Syntax int selectfor string code Select atoms using the supplied code which is inserted inside a loop over all atoms in the current model See the deselectfor command for a full description selectinsidecell 233 Syntax int selectinsidecell bool usecog FALSE Select all atoms whose coordinates are currently inside the confines of the unit cell if one exists If usecog is TRUE whole molecules are selected if their centre of geometry is within the unit cell The number of newly selected atoms is returned For example int n selectinsidecell selectioncog Syntax vector selectioncog Return the centre of geometry of the current atom selection For example vector v selectioncog primei Centrs ko Age ome oie Current SMS cto tg Sie sy Sie wos Voyo Wor p calculates and prints the centre of geometry of the current selection selectioncom Syntax vector selectioncom Return the centre of mass of the current atom selection For example vector v selectioncom newatom Be V X V Y V Z calculates the centre of mass of the current selection and creates a beryllium atom at those coordinates selectline Syntax 234 int selectline double Ix double ly double 1z double x double y double z double radius Selects
266. s original filename Save As Save the current model under a different filename Close Close the current model prompting to save first if changes have been made Copy Ctrl C Copy the current atom selection to Aten s internal clipboard Cut Ctrl X Copy the current atom selection to the clipboard and then delete it Paste Ctrl V Paste the contents of the clipboard to the current model at SS SGC the original coordinates The pasted atoms then become the current selection Note that pasted atoms are not translated to avoid overlap with existing atoms fi Delete Ctrl Delete Delete the current atom selection lt Stick Ctrl 1 Atoms are not explicitly drawn unless they possess no bonds bonds are drawn using simple lines e Tube Ctrl 2 Atoms and bonds are drawn as tubes P Sphere Ctrl 3 Atoms are drawn as uniformly sized spheres with bonds drawn as tubes o Scaled Ctrl 4 Atoms are drawn as spheres whose size depends on their atomic radii bonds are drawn as tubes 2 Individual Ctrl S Each atom is drawn according to its own assigned style 9 Box Select Escape Atoms may be de selected by clicking on them k individually or selected en masse with a click hold drag Molecule Bound fragments are selected by clicking on a single Select atom within that fragment Sn Element Clicking on a single atom selects all atoms of the same Select element el Expand The current selection is expanded by following bonds Selection attached to any select a
267. s with the rest of the molecules of the system 10 3 2 Pattern Granularity Patterns work on the basis of bound fragments molecules and a molecule cannot be split up smaller than this for instance in the examples above water cannot be represented by HO 1 H 1 since this would neglect a bond However there is nothing to stop a pattern crossing individual molecules Consider again the example 1 above Three further reiterating the point equivalent ways of writing the pattern description are HOHHOH 1 HOH 1 HOH 1 HOHHOH 1 HOHHOHHOH 1 Here we have encompassed individual molecular entities into supermolecular groups and as long as there are no bonds poking out of the pattern this is perfectly acceptable Although this coarse graining is a rather counter intuitive way of forming patterns it nevertheless allows them to be created for awkward systems such as that in 4 above We may write the following valid patterns for this arrangement of atoms HOHHHOHC1 1 HOH 1 HHOHC HOHHHO 1 HC1 1 Note that when automatically creating patterns if Aten stumbles across a situation that confuses it the default pattern of one supermolecule will be assumed i e X 1 where X is all atoms in the model This will work fine in subsequent energy calculations etc but will result in rather inefficient performance 266 11 Filters Filters determine the model trajec
268. same as any existing function or internal keyword e Since variables are strongly typed trying to set an integer variable from a string will not work since these are incompatible types However standard C style string conversion functions are available see String Commands in Section 9 28 94 So to initialise some variables assign values to them and print them out we would do the following oie abe doubbilernesiulitr a ALOP result i 5 0 Print Mama pits oy Si 0 Nes is e In addition to the standard int and double types a string variable exists for the storage of arbitrary length character strings and do not need to have a length specified on their creation they will adjust dynamically to suit the assigned contents Literal character strings should be surrounded by double quotes A set of variable types exist that are able to contain references not copies of various objects within Aten e g atoms models unit cells etc Variables of these types are declared in exactly the same way as normal variables see Section 8 2 for a list of available types A vector type is provided for convenience and stores a triplet of double values There is no boolean type use an int instead but the built in constants see Section 8 1 4 TRUE and FALSE may be used in assignment etc and correspond to the integer values 1 and 0 respectively All variables will default to sensible values e g empty string n
269. sen D S Maxwell and J Tirado Rives J Am Chem Soc 118 11225 11236 1996 W L Jorgensen and N A McDonald Theochem 424 145 155 1998 W L Jorgensen and N A McDonald J Phys Chem B 102 8049 8059 1998 R C Rizzo and W L Jorgensen J Am Chem Soc 121 4827 4836 1999 M L Price D Ostrovsky and W L Jorgensen J Comp Chem 22 13 1340 1352 2001 o E K Watkins and W L Jorgensen J Phys Chem A 105 4118 4125 2001 OO G O Note NETA definitions have been written for a large number of types in the forcefield but not all 12 2 5 Berensen et al Simple Point Charge Water spc ff Rigid simple point charge model for water References o H J C Berendsen J P M Postma W F van Gunsteren and J Hermans in Intermolecular Forces B Pullman ed Reidel Dordrecht 1981 p331 12 2 6 Berensen et al Extended Simple Point Charge Water spce ff 291 Simple point charge model for water modified to reproduce molecular dipole in the liquid phase References o J C Berendsen J R Grigera and T P Straatsma J Phys Chem 91 6269 6271 1987 12 2 7 Rappe et al Universal Forcefield uff ff Universal forcefield for the whole periodic table by Rappe et al References o A K Rappe C J Casewit K S Colwell W A Goddard II and W M Skiff J Am Chem Soc 114 10024 10039 1992 Notes o Generated terms should be checked by hand if forcefield expressions are expor
270. setcoords Syntax void setcoords double x double y double z void setcoords double x double y double z int id Set the coordinates of the current or specified atom setelement Syntax void setelement string int element void setelement string int element int id Set the element of the current or specified atom setforces Syntax void setforces double fx double fy double fz void setforces double fx double fy double fz int id Set the forces of the current or specified atom 133 setfx Syntax void setfx double d void setfx double d int id Set the x force of the current or specified atom setfy Syntax void setfy double d void setfy double d int id Set the y force of the current or specified atom setfz Syntax void setfz double d void setfz double d int id Set the z force of the current or specified atom setid Syntax void setid int newid void setid int newid int id Set the temporary ID of the current or specified atom useful for when parsing atoms from a file that are not in any useful order but have an id specified for the purposes of subsequent connectivity definitions for example Within filters once loading is complete the finalisemodel command will reset all atom ids to internal numbering setrx Syntax void setrx double d v
271. sic box select interaction mode Select all atoms in the current model Copy the current atom selection to the clipboard Centre the current atom selection at 0 0 0 Deselect all atoms in the current model Delete the current atom selection Fold all atoms into the unit cell Fold atoms into the unit cell keeping molecules intact Hide all selected atoms Unide any hidden atoms Toggle the selection state of all atoms Create a new empty model Load an existing model into Aten Play pause current trajectory Reset the camera for the current model Save the current model under its original filename Paste the contents of the clipboard to the current model Copy the current selection to the clipboard and delete it Redo last undone operation Undo last operation View models as sticks View models as tubes View models as tubes and spheres View models as tubes and scaled spheres View models according to atom s assigned styles Zoom out Zoom in Jump to first frame of current trajectory Jump to last frame of current trajectory Toggle detection and display of hydrogen bonds Raise a dialog window allowing a quick command to be run 57 7 4 The Main Toolbar The main toolbar provides quick access to model load save edit and selection operations Left to right these icons are Shortcut Description New Ctrl N Create a new empty model Open Ctrl O Load an existing model into Aten Save Ctrl S Save the current model under it
272. string type i string type j double datal we Add a bond definition to the current forcefield form should correspond to one of the implemented bond functional forms while the two types refer to either type or equivalent names of defined atom types Up to ten data parameters may be supplied 170 clearexportmap Syntax void clearexportmap Clear any manual export typemap definitions For example clearexportmap clearexpression Syntax void clearexpression Removes any forcefield expression defined for the current model For example clearexpression clearmap Syntax void clearmap Clear any manual typemap definitions For example clearmap cleartypes Syntax void cleartypes Clear any previously assigned atom types from the current model For example cleartypes 171 createexpression Syntax int createexpression bool nointra FALSE bool nodummy FALSE m bool assigncharges TRUE Creates a suitable energy description for the current model The optional flags control exactly what is in the created expression or how it is created The nointra flag can be used to force the creation of an expression containing only atomtype i e van der Waals terms in such a case patterns will contain no definitions of intramolecular bonds angles and torsions whatsoever The nodummy option indicates whether dummy intramolecular
273. suring tool able to measure distances angles and torsions in the model depending on how many arguments are supplied Note that the resulting measurement is added to the Model s internal list and will be displayed in the model Also note that measuring the same thing between the same atoms twice will remove the measurement from the Model For example double rij measure 1l 2 returns the distance between atoms and 2 double theta measure 10 20 30 returns the angle between atoms 10 20 and 30 double phi measure 9 8 7 6 measure 9 8 7 6 returns the torsion angle made between atoms 9 8 7 and 6 and then instantly removes it from the model by measuring it again measureselected Syntax void measureselected int natoms This command is a general measuring tool to measure all of one particular type of interaction i e bond distances angles or torsions within the current atom selection The single argument specifies the type of interaction to calculate by specifying thu number of atoms involved in the interaction i e 2 3 or 4 for bond distances angles and torsions respectively 201 For example measureselected 3 calculates and displays all bong angles in the current atom selection 202 9 19 Messaging Commands Output messages from command lists filters All commands work like the C printf command and accept the same fundamental format specifiers All output
274. system Here there is only one choice the water model we created earlier so select it ans press Next Be Disorder Wizard ooo Step 5 5 Set Component Populations Set the desired population number andlor density for each component Water Target Partition 0 Whole Cell v Policy both ESA 20 Finally the most important step of the wizard is to define a policy for the insertion of each model we selected in the last step There are usually four options here either a specific number of molecules or a specific density more correctly a specific partition density and exact number and density or a relative number and exact density Since our cell size is to be automatically determined only one of those four options is available Exact Number Density since both pieces of information are required in order to work out the final cell volume So choose the number of water molecules to add say 200 and the density you want them to have in the cell Press Finish and the system will then be built A Aten vL7 r1671 Disorder Model lt lt no filename gt gt Modified Y DY File Edit View Selection Model Trajectory Forcefield Settings Scripts Help Jan Se DR twHm3 e sea 205 amp Select Click or click drag to select shift toggle left click or add soa selection left click drag or translate middle click 600 Atoms 3603 000000 g mol drag or rotate in local frame right click drag etri remove from selectior
275. t 20 0 sets the next grid point value to be 20 0 finalisegrid Syntax void finalisegrid Perform internal post load operations on the grid Must be called for every new grid after all data has been read in For example 187 finalisegrid gridalpha Syntax double gridalpha double gridalpha double newalpha Set the alpha value transparency of the current surface with 0 0 being fully opaque and 1 0 being fully transparent i e invisible or simply return the current alpha value if no new value is provided Note that this command sets the alpha values for both the primary and secondary surface colours For example gridalpha 0 5 gridaxes Syntax void gridaxes double ax double ay double az double bx double by double bz double cx double cy double cz Set the axes of the current grid specified as three vectors For example Giricewes IL O O O 1 0 0 0 Wye sets a cubic system of axes for the current grid gridaxes 0 8 0 0 0 1 0 6 0 0 O 0 7 sets a monoclinic system of axes for the current grid gridcolourprimary Syntax void gridcolourprimary double r double g double b double a 1 0 Set the internal colour of the primary grid surface to the RGB A value each component of which should be in the range 0 0 to 1 0 inclusive 188 For example gridcolourprimary 1 0 1 0 0 0 sets the primary surface colour to yellow
276. t description of their meaning I i interactive 48 Starts Aten in interactive mode where commands are typed and immediately executed The GUL is not started by default but may be invoked int lt name value gt Creates a floating integer variable name See the double switch for a full description K k keepview Preserves the last stored view of models when the GUI starts retaining any model rotations and camera transformations performed in scripts or on the command line normally the view is reset to display the entire model on startup keepnames If specified for each model loaded the original atom names in the file will be preserved as a series of forcefield types generated within a new forcefield created specifically for the model Elements are still determined from conversion of the atom names and may still be mapped with the map option This option is useful for quickly creating a skeleton set of forcefield types from an existing model with type names or to allow quick import and export of typed configurations without requiring the original forcefield file to be loaded Note that the keeptypes and keepnames switches are mutually exclusive keeptypes If specified for each atom name converted to an element using a forcefield name match the corresponding forcefield type will be assigned to the atom and fixed Like the keepnames switch this is useful for preserving atom type data when
277. t has a specific 113 componentpartition componentpopulation distances eigenvectors energy ff ffangles ffbonds ffmass fftorsions fftypes frame frames glyphs grids id mass name nangles natoms nbasiscartesians nbasisshells nbonds ndistances nffangles nffbonds nfftorsions int int measurement eigenvector energystore cat forcefield ffbound ffbound ffbound ESF atom model model glyph grid int double string int 114 density requested FALSE The integer index of the partition which this model will be added to in the disordered builder The number of times this model will be added to the specified partition in the disordered builder List of current distance measurements in the model List of current eigenvectors stored in the model The model s energy store containing the total calculated energy and all associated contributions Forcefield associated to the model if any List of unique forcefield angle terms in the model List of unique forcefield bond terms in the model Forcefield mass of the current model which can differ from the actual mass if united atom types have been assigned List of unique forcefield torsion terms in the model Array of unique atom types used in the model The current frame in the model s trajectory if it has one Array of trajectory frame pointers only 1f
278. te the new supercell Y Build Back in the Build Window go to the Edit page and Rebond the model A Aten vL7 11671 Unnamed001 lt lt no filename gt gt Modified Y Y Y File Edit View Selection Model Trajectory Forcefield Settings Scripts Help UA DY DR H eee VQAneG ae ws OR a x wt We aa Te RU ran V 4 yh Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle 540 Atoms 11011 788000 g mol click drag or rotate in local frame right click drag ctrl remove from selection Parallelepiped 3 603856 g cm 25 Script newmodel alumina CSL sd 2904 5 622 GO MOS 83 O newatomfrac Al 0 6595 0 0 3165 newatomfrac Al 0 9166 0 0 2073 newatomfrac 0 0 8272 0 0 4272 newatomfrac 0 0 495 0 0 2526 newatomfrac 0 0 1611 0 0 0984 spacegroup C2 m pack oler 0 033 3 rebond Y 26 5 3 Creating an NaCl Water Two Phase System GUI It s often necessary to create a larger system from a simple or complex unit cell for example to generate bulk supercells of crystals sufaces etc The method outlined below shows how to do this for a simple crystal and then extends this system to create a solid liquid interface Create the Template Model First off we will create a basic FCC template model which has a unit cell of exactly 1 A with atoms at 0 0 0 0 5 0 5 0 0 0 0 5 0 5
279. ted o Detection of some atomtypes namely transition metals is imperfect o Warning Generation of terms especially angles needs to undergo proper testing If you wish to help please contact me 12 2 8 Mayo Olafson amp Goddard II s Generic Forcefield testing dreiding ff Universal forcefield for the whole periodic table References o S L Mayo B D Olafson and W A Goddard II J Phys Chem 94 8897 8909 1990 Notes o dreiding ff currently lives in the testing directory since it is a rule based forcefield and is currently being rewritten o Generated terms should be checked by hand if forcefield expressions are exported o Detection of some atomtypes namely transition metals is imperfect o Warning Generation of terms especially angles needs to undergo proper testing If you wish to help please contact me 12 2 9 General Amber Forcefield testing gaff ff General Amber forcefield containing precalculated terms for most intramolecular terms and generator section for any that are missing References 292 o J Wang R M Wolf J W Caldwell P A Kollman and D A Case J Comp Chem 25 1157 1174 2004 Notes o gaff ff currently lives in the testing directory since it s rule based part has not been implemented yet 12 2 10 Liu Wu amp Wang s United Atom Ionic Liquids Forcefield lww il ff United atom ionic liquids forcefield for a handful of cations and anions References o X
280. termining multiple bonds based on the valency of atoms and aromaticity based on double bonds in rings For example augment Augment method for a description of the rebonding algorithm implemented in Aten bondtolerance Syntax double bondtolerance double bondtolerance double tol Adjust the bond calculation tolerance It may often be necessary to tweak the bond tolerance in order to get Aten to recognise patterns within models correctly The current or new bond tolerance is returned For example bondtolerance 1 20 sets the bonding tolerance to 1 2 double tol bondtolerance retrieve the current bond tolerance Rebond method for a description of the rebonding algorithm implemented in Aten clearbonds Syntax 137 void clearbonds Delete all bonds in the current model For example clearbonds clearselectedbonds Syntax void clearselectedbonds Delete all bonds in the current atom selection For example clearselectedbonds newbond Syntax void newbond atom int i atom int j void newbond atom int i atom int j string int bondtype Create a new bond in the model between the specified atoms The optional bondtype argument specified the type of bond e g single default double or triple Alternatively an integer number representing the bond order may be given For example newbond 4 5 double creates a double bond betwe
281. terms of simple functional form and with all parameters set to zero should be automatically added to the energy expression should no suitable terms be found in the associated forcefield s Finally assigncharges specifies whether to assign charges to atoms from their assigned forcefield types TRUE or to leave atomic charges as they currently are FALSE wa For example createexpression deleteff Syntax void deleteff string forcefield ff Delete the specified forcefield i e unload it equivalents Syntax void equivalents string name string typename s Define equivalent terms in the current forcefield name is the new typename to which the list of quoted typenames are linked for subsequent use in intramolecular term definitions See the equivalents forcefield keyword for more information exportmap Syntax void exportmap string maps Set up manual mappings that convert atomtype names when expression are exported Works in the opposite way to the map command For example 172 map CT Ctet N3 N converts the atomtype names CT and N3 so that they appear as Ctet and N in any expression files written out ffmodel Syntax void ffmodel Associates current forcefield to the current model For example ffmodel ffpattern Syntax void fpattern string pattern void fpattern int patternid void fpattern pattern p Associates
282. tern and placed at the geometric centre of the atom IDs given in atomlist If no atoms are given the centre of geometry of all atoms is used The new site becomes the current site For example newsite watercentre h2o0 239 adds a site called watercentre based on the pattern called h20 and located at the centre of geometry of all atoms newsite oxy methanol 5 adds a site called oxy based on the pattern called methanol and located at the fifth atom in each molecule siteaxes Syntax void siteaxes string x atomlist string y atomlist Sets the local x first set of atom IDs and y second set of atom IDs axes for the current site Each of the two axes is constructed by taking the vector from the site centre and the geometric centre of the list of atoms provided here The y axis is orthogonalised with respect to the x axis and the z axis constructed from the cross product of the orthogonal x and y vectors For example Sirenas Mil 247 MU sets the x axis definition of the current site to be the vector between the site centre and the average position of the first two atoms and the y axis definition to be the vector between the site centre and the position of the sixth atom 240 9 28 String Commands Manipulation and conversion of string variables afterstr Syntax string afterstr string source string search bool sourceonfail FALSE Return the part of t
283. th various tool windows These tool windows are accessed by the ToolBox widget which by default is the only window displayed on startup if it is not visible you can raise and centre it on the main window from the menu item Settings Show Toolbox At the foot of the window is a status bar reflecting the content of the current model listing the number of atoms and the number of selected atoms bold value in parentheses but only if there are selected atoms the mass of the model and the cell type and density if the model is periodic Toolbox o x A Aten v1 7 1603 Unnamed001 lt lt no filename gt gt Y a OX Tat Model List af Atom List Command File Edit View tion Model Trajectory Forcefield Settings Scripts Help 23 Z Matrix Messages LJ w m i X oS p fi 9 2 IN Q Ss PE e gt Edit YE Build a Transform x Fragments 3 Position Define Transform amp Disorder Calculate Modify 2 P bom Geometry Y FF Energy D Selection 2 2 MD Visualise a Grids Re Glyphs S Vibrations CEB Trajectory Select Click or click drag to select shift toggle left click or add area to selection left click drag or translate middle click drag or 0 Atoms 0 000000 g mol rotate in local frame right click drag ctrl remove from selection Non periodic Figure 7 1 Aten s main window and toolbox The edges of the main window around the canvas are standard
284. the four possible values specified either check run restart or analyse 274 Setting Options All variables set from an option statement are guaranteed to take on at least the default value of the control when the filter or script executes From the GUI it is possible to change the values of defined options since an options dialog is presented once load save filenames are selected and immediately before the filter actually executes From the command line it is also possible to set options within the filter whenever a filter nickname is provided e g as for the first argument to the savemodel command a list of variables and the value they should take can be provided as part of the string Let us assume that there is a filter whose definition is as follows filter type exportmodel extension crd nickname crd Define some options me 1 Orig NoMa An eS Enu O 10 il Zip string type option Style combo alpha beta gamma 1 Saving a file in this format without setting any of the options would be done with the following command SAVEMO SIE y stab es iateh 9 The two variables n and type can be set to different values in the following way savemodel crd n 6 type beta my file crd Option Types All available control types are listed in the following table Note that all of the required data items must be given as arguments followin
285. the matrix elements ax ay az cz to the given value For example setcell beta 101 0 sets the cell angle beta to 101 degrees setcellt ars 15 5 3 sets the cell length a to 15 5 A spacegroup Syntax void spacegroup int string sg Sets the spacegroup of the model used for crystal packing For example spacegroup 12 sets the model spacegroup to be C2 m number 12 spacegroup P1 m sets the model spacegroup to P1 m 152 9 5 Charges Commands Assign partial charges to models atoms and patterns charge Syntax double charge double charge double q Assigns a charge of q to each selected atom in the current model or returns the total charge of the current selection if no value is supplied For example charge 1 0 gives each atom in the current model s selection a charge of 1 0 chargeff Syntax void charge Assigns charges to all atoms in the current model based on the forcefield associated to the model and the current types of the atoms For example chargeff chargefrommodel Syntax void chargefrommodel Copies charges of all atoms in the current model to the atoms of the current trajectory frame For example chargefrommodel 153 chargepatom Syntax void chargepatom int id double q Assigns a charge of gto atom idin each molecule of the current pattern For example chargepatom 3 0 1
286. the trajectory is cached List of glyphs owned by the model List of grids owned by the model The index of the model in Aten s internal list of loaded models Mass of the current model Name of the model Number of angle measurements in the model Number of atoms in the model Number of cartesian basis functions defined in stored basis shells Number of basis shells defined in the model Number of bonds in the model Number of distance measurements in the model Number of unique angle terms used in the model Number of unique bond terms used in the model Number of unique torsion terms used in the model nfftypes int Number of unique atom types used in the model nframes int Number of frames in associated trajectory nglyphs int Number of glyphs owned by the model ngrids int Number of grids owned by the model npatterns int Number of patterns defined for the model nselected int Number of atoms selected in the model ntorsions int Number of torsion angle measurements in the model nunknown int Number of atoms in the model that are of unknown element patterns pattern Array of patterns currently defined for the model selection atom A list of atoms in representing the current atom selection of the model torsions measurement List of current torsion angle measurements in the model 8 2 32 Model Type Functions addhydrogen Syntax void addhydrogen Hydrogen satisfy all atoms in the model See the add
287. tinct sets of commands those which measure and those which calculate geometry The former create visible measurements within the model which can then be viewed in the GUI while the latter simply determine and return geometric values Both sets take a variable number of arguments which determine whether a distance angle or torsion is measured determined clearmeasurements Syntax void clearmeasurements Clear all measurements in the current model For example clearmeasurements geometry Syntax double geometry atom int i atom int j atomlint k 0 atomlint 1 0 This command is a general measuring tool able to measure distances angles and torsions in the model depending on how many arguments are supplied Note that unlike the measure command the resulting measurement is not added to the Model s internal list and thus will not be displayed in the model For example double rij 50 icone ime aio K507 srirak sealapl ab Geon cy lab calculates the distances between the first 50 atoms in the model and the first regardless of whether they are bound or not listmeasurements Syntax void listmeasurements 200 List all measurements in the current model For example listmeasurements prints out a list of measurements made so far measure Syntax double measure atom int i atom int j atom int k 0 atom int 1 0 This command is a general mea
288. tion onebond onebond requests that the atom has exactly one bond of any type linear Two bonds to the atom in a linear arrangement angle i j k gt 170 tshape Three bonds to the atom in a tshape geometry with two bonds making an angle gt 170 trigonal 314 Three bonds in a trigonal planar arrangement with the largest of the three angles between 115 and 125 tetrahedral tetrahedral geometries are possible for atoms with exactly two bonds making an angle between 100 and 115 exactly three bonds with the largest of the angles between 100 and 115 and exactly four bonds to the atom with the average of the angles laying between 100 and 115 sqplanar Four bonds to the atom in a square planar sqplanar arrangement with the average of the angles laying between 115 and 125 tbp Five bonds to the atom are assumed to be trigonal bipyramidal tbp geometry octahedral Six bonds to the atom are assumed to be in an octahedral arrangement 315 13 Functional Forms All forcefield term functional forms are listed in the following sections along with their parameters default values for which follow in brackets if they exist 13 1 VDW Functional Forms Table 13 1 VDW Functional Forms NEME Keyword Form Param Rule Lennard Jones 12 6 1j Uij 4e or l2 or Geom 6 o Arith Lennard Jones 12 6 ljgeom Uy 4e or 12 or Geom Geometric rules 6 o Geom Inv
289. tly two bonds amp is bound to a hydrogen amp is bound to another hydrogen Similarly a water hydrogen HW is a hydrogen bound to an oxygen atom that has two bonds to it and is bound to a hydrogen and is bound to another hydrogen In the type descriptions above the dash is short hand for saying is bound to while the bracketed part after 0 in the water hydrogen description describes the required local environment of the attached oxygen Using brackets to describe more fully the attached atoms is a crucial part of atom typing and may be used to arbitrary depth so for example we could add a bracketed description to the hydrogen atoms as well if there was anything left to describe If necessary descriptions can be written that uniquely describe every single atom in a complex molecule by specifying completely all other connections within the molecule This should not be needed for normal use however and short descriptions of atom environment up to first or second neighbours will usually suffice 305 Example 2 3 hydroxypropanoic acid Assuming that the OH group in the carboxylic acid functionalisation will have different forcefield parameters to the primary alcohol at the other end of the molecule here we must describe the first and second neighbours of the oxygen atoms to differentiate them To begin we can describe the carbon atoms as either two or three different types either methylene carboxylic aci
290. to a regular grid No grid size specification is necessary Label Types 329 Valid label types are as follows Table 16 12 Label type keywords Value Description charge Atomic charge currently assigned to the atom element Element symbol of the atom ffequiv Forcefield equivalent name from the assigned forcefield atom type or the forcefield atom type name if no equivalent applies id Integer atom ID type Assigned forcefield atom type name if any 16 13 Output Types Valid output types or debug modes are as follows Table 16 13 Output type keywords Value Description all Enable output of all types listed in this table calls Print out entrances and exits to most subroutines to enable quick tracing of crash locations commands Trace execution of commands in command lists e g filters and print information on variable access paths gl Debug OpenGL calls and graphics capabilities as best as is possible parse Debug file reading and argument parsing routines typing Print lots of information regarding setting and matching of atom type descriptions verbose Enable a little extra output but not much 16 14 Parse Options These options determine how general parsing of plain text files proceeds as well as controlling delimited argument parsing Table 16 14 Parse option keywords Value Description usequotes Phrases enclosed in quotes will be parsed as single arguments skipblanks Blank lines or those cont
291. to find which ids are currently in use name Syntax name long name of filter Sets the long name of the filter to be used as the filetype description of files identified by the filter This name will appear in the file type lists of file dialogs in the GUI and also in the program output when reading writing files of the type For example name SuperHartr Coordinates File nickname Syntax nickname short name of filter Sets a nickname for the filter which allows it to be identified easily in the command language and importantly from the command line It should be a short name or mnemonic that easily identifies the filter No checking is made to see if a filter using the supplied nickname already exists For example nickname shart sets the nickname of the filter to shart nickname zyx sets the nickname of the filter to zyx search Syntax search string to search 271 Occasionally checking the contents of the file is the easiest way to determining its type and is probably of most use for the output of codes where the choice of filename for the results is entirely user defined For example most codes print out a whole load of blurb and references at the very beginning and usually searching for the program name within this region is enough to identify it For files that are only easily identifiable from their contents and not their filename plain text search
292. to insert into and should be selected as the current model in the main view The Build button will only be available if the current model is periodic Note that the current model does not have to be empty to begin with but if it is not a forcefield must be assigned or must be available that describes completely the existing contents 71 By default all components are randomly distributed over the entire space of the model cell but can be restricted to specific regions of the cell if required For the model currently selected in the list of components the Region panel may be used to define an area of the unit cell in which to restrict insertions of the model If regions are defined for one or more models these will displayed in the current model s cell The number of cycles determined the number of times to perform a round of Monte Carlo moves see XXX while the VDW Scale sets a temporary scaling factor to use in the energy calculation 72 7 12 Forcefields Window The Forcefields is the place to go to load in and edit forcefields perform atom typing on models and calculate minimise the energies of models As well as being able to perform standard steepest descent and conjugate gradient minimisations Aten also provides a molecular Monte Carlo minimiser and the ability to run MOPAC directly from the GUI Energy Forcefields o x Energy Forcefields o x Energy Forcefields Manual Typing Energy Forcefields Manual Typi
293. to read gridded volumetric or surface data from files Any grids created in these sections must have the finalisegrid command called on them otherwise they will not be registered 272 properly within the program importmodel Describes how to import model data including atoms cell and spacegroup data bonds glyphs etc Any models created in importmodel filters must have the finalisemodel command called on them otherwise they will not be registered properly within the program importtrajectory Read frames from trajectory files See the section on trajectories Section 11 2 for additional information on how trajectories are handled within Aten For example type importgrid type exportmodel within Syntax within n Defines the maximum number of lines at the beginning of the file that will be searched for string definitions default is 10 For example within 50 specifies that the first 50 lines should be searched for identifying strings zmap Syntax zmap zmaptype By default it is assumed that the commands which create new atoms will be given a proper element symbol from which to determine the atomic number Case is unimportant so na Na and NA will all be interpreted as atomic number 11 sodium Where element symbols are not used in the model file there are several alternative options that tell these commands how to convert the element data they are passed into atomic numbers For exam
294. tom List Window Atom Selection The selection of items in the atom list mirrors the selection in the current model de selecting atoms in one will also de select them in the other If patterns are defined de selecting the pattern name in the list de selects all atoms making up the pattern Changing the Order of Atoms The four buttons at the foot of the atom list allow the current selection of atoms to be moved up and down the list useful for reordering atoms into a specific sequence Selected atoms can be shifted up down the list one place at a time or all moved to the top or bottom of the list at once In the latter case the order of the original selection is preserved 61 7 7 Build Window The primary function of the Build window is to allow for drawing deletion and transmuting of individual atoms and bonds using the mouse along with drawing and automatic creation of bonds Build Tools o x Edit Tools Options Draw Atom 4 A Chain gt Frag n i Delete A Transmute AddH HEMA Be Pick Transmute Sel AddH Model Bonding S Single gf Double Triple E Delete 11 Augment o Rebond w aa Clear Figure 7 4 Build Window Edit controls The top half of the Edit page of the window provides tools to draw individual atoms chains of atoms and molecular fragments allow the deletion and transmutation of atoms and provide the ability to add hydrogen atoms automatically t
295. tom int i atom int j atom int k double angle Adjusts the angle made between atoms i j k so that it becomes the target value moving the atom k and all its direct and indirectly bound neighbours except i and 7 The coordinates of atom i and j remain unaffected This operation can only be performed when atoms j and x are not present in the same cyclic structure The atoms i j and k do not have to be bound so it is possible to move separate fragments relative to each other using this method For example Sestao Ls LO Wal 12 109 3 7 sets the angle made between atoms 10 11 and 12 to be 109 5 setdistance Syntax void setdistance atom int i atom int j double dist Shifts the atom j and all its direct and indirectly bound neighbours except i so that the distance between i and j is dist The coordinates of atom i remain unaffected This operation can only be performed for atoms which are not present in the same cyclic structure e g trying to set the distance of two atoms in a benzene ring is not allowed However note that the two atoms i and j do not have to be bound so it is possible to move separate fragments further apart by this method For example 255 setdistance 1 4 4 9 sets the distance between atoms 1 and 4 to be 4 9 A translate Syntax void translate double dx double dy double dz Translates the current selection by the specified vector For example transitoria MOMO
296. toms Invert Ctrl I Toggle the selection state of all atoms Selection 58 7 4 1 The Mouse Toolbar There is only one other toolbar in newer versions of Aten the Mouse toolbar For multi button mice each button can be assigned an invidual action select rotate model etc For those who use single button rats this toolbar changes the function of the first or left button between select interact rotate model and translate model Selecting these buttons overwrite the stored action for the left button in the Preferences Icon Shortcut Action fre Fl The left button selects and interacts with atoms F2 The left button rotates the view or selection lt gt F3 The left button translates the view or selection 59 7 5 The ToolBox The ToolBox provides access to most of Aten s functionality allowing various different subwindows to be shown and hidden Toolbox o x Es Model List gs Atom List E Command z Z Matrix Messages Edit FE Build a Transform S Fragments 3 Position a Define Transform amp F Disorder t o KO Calculate Modify Geometry y FF Energy Selection bo _ _ __ A _ _ A o l E MD 2 Visualise a Grids Ps Glyphs A Vibrations IPEN Trajectory Figure 7 2 The ToolBox Window Button Window Function Contents gt Model List List of models currently loaded Tat Atom List List of atoms in the current model E Command Runs single commands
297. tory grid surface and forcefield expression formats that Aten can read and write They are essentially small programs written in Aten s internal command language based syntactically on C and are stored as plain text files These files are parsed and compiled when Aten starts up This has several advantages e Users may add support for their own particular formats at will e No recompilation of Aten is necessary when adding new filters or adjusting old ones e Potentially any file format can be supported even binary formats With this flexibility of course come some modest disadvantages e Speed the C style code contained within filters is strictly speaking interpreted it is by no means as fast as properly compiled code e File formats that need particularly awkward operations requiring a more complete C language may be difficult to implement These two points aside though filters make Aten a powerful and flexible tool adaptable to conform to many different program code input and output formats As mentioned the programming language used by filters is essentially a subset of C implemented with the same syntax and style see the command language overview in Chapter 9 for a description but includes several hundred custom commands to control Aten in order to build up atoms in models access data etc So if you already know C or C writing a filter should be a breeze If you don t it s not too difficult to pick up
298. ts the shell variable count as an integer number gui Syntax void gui Starts the GUI e g from a script if it isn t already running For example gui help Syntax help command Provide short help on the supplied command For example help cellaxes null 247 Syntax void null variable var The null command accepts one or more pointer variables whose values are to be set to NULL 0 searchcommands Syntax void searchcommands string search Search all available commands for the partial command name specified seed Syntax void seed int i Sets the random seed For example seed 3242638 quit Syntax void quit Quits out of the program For example quit 248 9 30 Trajectory Commands Open and associate trajectory files to models and select frames to display edit from the current trajectory Trajectories for information on how trajectories are handled within Aten addframe Syntax model addframe model addframe string title Append a new trajectory frame to the current model s trajectory The reference to the new frame is returned For example model m addframe new config cleartrajectory Syntax void cleartrajectory Clear any associated trajectory and frame data in the current model For example cleartrajectory firstframe Syntax void firstframe
299. ubsequently created using name as the element are automatically converted to the corresponding element For example map CT1 C CT2 C converts atoms with names CT1 and CT2 to carbon newff Syntax forcefield newff string name Create a new empty forcefield with the given name and make it current Returns a reference to the new forcefield For example forcefield ff newff testff printsetup Syntax void printsetup Prints the current expression setup For example printsetup recreateexpression Syntax E void recreateexpression bool nointra FALSI Delete and recreate a suitable energy description for the current model The optional nointra flag can be used to force the creation of an expression containing only atomtype i e van der Waals terms For example 176 recreateexpression rules Syntax void rules string ruleset Set rules set to use for parameter generation in the current forcefield see forcefield fules for more info Note The implementation of rule based forcefields will change in a future release saveexpression Syntax int saveexpression string filter string filename Export the forcefield expression for the current model in the format determined by the filter nickname to the filename specified Return value is 1 for successful write or 0 otherwise For example saveexpression dlpoly dat
300. ul when Aten is creating expressions and searching for specific interactions between atom types as soon as an intramolecular definition is found that matches it is used and no further searching is done So loose definitions involving wildcards should be put near to the end of the block in which they occur 301 12 4 Rule Based Forcefields Forcefields exist where individual intramolecular parameter definitions i e those provided by the bonds angles and torsions blocks are not necessary Instead such parameters are constructed as and when necessary using a set of parameters that depend only on the atomtypes involved These forcefields are so called rule based and are often able to describe enormously varied systems from a small set of defining parameters Rule based forcefields are defined in exactly the same way as normal forcefields save for the lack of blocks that define intramolecular terms Instead the per atomtype parameters must be provided instead and for all atomtypes defined in the types section s This generator data is then used by the equations defined within the code to construct the necessary intramolecular terms when required One or more data blocks should be used to define this data for each atomtype 12 4 1 Functions In a rule based forcefield all the useful function declarations which calculate the correct parameters usually from values supplied in a data block must be made within a single function blo
301. umber of cartesian basis functions implied by the current basis shell definitions of the model For example igenvector neweigenvector 180 creates a new eigenvector which will contain 180 coefficients 207 newvibration Syntax vibration newvibration string name auto Adds a new empty vibration definition to the current model printzmatrix Syntax void printzmatrix Prints a Z matrix for the current model to the console creating one first if necessary 208 9 22 Model Commands Model creation and management createatoms Syntax void createatoms Can be run when importing trajectory frames Creates enough atoms in the current trajectory frame to match the parent model For example createatoms currentmodel Syntax model currentmodel model currentmodel int id model currentmodel string name model currentmodel model m Returns a reference to the current model if no argument is given or selects the supplied model and makes it the current model The model may be selected either by name by its integer position in the list of loaded models i e 1 to N or a model type variable containing a valid model reference may be passed For example currentmodel 4 selects the fourth loaded model currentmodel Protein coordinates selects the model named Protein coordinates provided it exists model ml m2 ml newmodel Test m
302. umbers equal to zero on initialisation To create a variable with a specific value simply do the following int i 1 3 2 k 1001 double myvar 0 0 angle 90 0 8 1 3 Arrays Arrays of most variable types are allowed some for instance the aten type don t really make sense as an array Arrays are requested by providing a constant size or an expression in square brackets after the name int values 100 i 4 double q il Here two arrays are created an array of 100 integer numbers called values and an array of four floating point numbers called g Array indices always run from to the size of the array unlike C in which arrays run from 0 to N 1 Note that it is not possible to use a custom range of array indices as is the case in Fortran Arrays can be initialised to a simple value on creation setting all elements to the same value string s 4 Nothing 95 Or each element to a different value using a list enclosed in curly brackets Sin Sf NO Pt NC Wieck Yio 2 samsacgea ip Also all array elements can be set to the same value with a simple assignment tas LOO t 40 8 1 4 Predefined Constants Several predefined constants exist and may not be overridden by variables of the same name All predefined in constants are defined using uppercase letters so the lower case equivalents of the names may be used as variables functions etc Table 8 1 Built In Constants NET Type Value ANGBOHR
303. urrent or specified atom s position as data n in the current glyph For example ypt onni yam oo ey links the 55th atom s position to the third datum in the current glyph glyphatomv 182 Syntax void glyphatomv int n void glyphatomv int n atom int sourceatom Set current or specified atom s velocity as data n in the current glyph For example atom i newatom H glyphatomv 2 1 links the velocity of new atom i to the second datum in the current glyph glyphatomsf Syntax void glyphatomsf atom int sourceatom Accepts one or more atoms setting consecutive data in the current glyph to the forces of the atoms atom IDs provided For example gil pRaronst ZONE links the forces of atoms 1 2 and 3 to the first three glyph data glyphatomsr Syntax void glyphatomsr atom int sourceatom Accepts one or more atoms setting consecutive data in the current glyph to the positions of the atoms atom IDs provided For example glyphatomsr 3 10 links the positions of atoms 3 and 10 to the first two glyph data glyphatomsv Syntax 183 void glyphatomsv atom int sourceatom Accepts one or more atoms setting consecutive data in the current glyph to the velocities of the atoms atom IDs provided For example gl prRartons y Li LI links the velocities of atoms 9 11 and 13 to first three glyph data glyphcolour Syntax
304. ved while the interval value determines the stride between frames i e 1 for every frame 2 for every other frame 10 for every tenth frame etc For example savemovile Mitra mo O24 OA mi OO ON saves a movie called traj mpg with size 1024x1024 beginning at frame 50 and writing every 50th frame until frame 1000 195 9 16 Labeling Commands Add and remove atom labels clearlabels Syntax void clearlabels Remove all atom labels in the current model For example clearlabels label Syntax void label string type Adds the specified label to each atom in the current selection Valid types are listed in Label Types For example label element adds element labels to the current atom selection removelabel Syntax void removelabel string type Remove the specified label if it exists from each atom in the current selection For example removelabel equiv removes the forcefield equivalent type label from each atom in the current selection 196 9 17 Math Commands Standard mathematical functions abs Syntax double abs int double num Returns the absolute positively signed value of num cos Syntax double cos double angle Returns the cosine of angle which should be given in degrees dotproduct Syntax double dotproduct vector u vector v Calculate and return the dot product of the two vectors u and v
305. void glyphcolour int n double r double g double b double a 1 0 Set the colour of vertex n for the current glyph to the RGB A colour provided each component of which should be in the range 0 0 to 1 0 inclusive For example Gilgyjoleolko ula iO OOOO sets the colour of the first vertex in the current glyph to red glyphdata Syntax void glyphdata int n double r double g double b Set vector data n for the current glyph to the fixed values provided For example cuac OF Omori Olmert sets the first positional data in the glyph to 0 0 5 0 2 4 glyphsolid Syntax void glyphsolid bool issolid 184 Sets the drawing style of the current glyph to solid true or wireframe false if the glyph style permits For example glyphsolid true glyphtext Syntax void glyphtext string text Set the text data in the current glyph For text style glyphs this is a necessary piece of data For example glyphtext Coordinate Origin newglyph Syntax glyph newglyph string style string options Create a new glyph of the specified style and make it current The colour of the glyph is set using the default glyph colour set in the global preferences Valid glyph styles are listed in glyph types Positional size scale vector data should be set afterwards with appropriate glyphatom and glyphdata commands One or more options may be given to the co
306. voked by providing the batch and export switches together batch export allows a series of commands to be run on a set of loaded models the results of which are then saved in new files in the model format provided to the export switch The GUI is not automatically started in batch export mode Let s say that you have a directory full of xyz files that you wish to energy minimise with MOPAC2009 see Section 14 2 centre at zero and then save as input to GAMESS US This can be achieved with the following command bob pc gt aten export gamusinp batch c mopacminimise selectall CONTEST Various export options for the GAMESS US filter e g method type basis set can be set at the same time See how to set filter options in Section 11 1 5 and Section 5 11 for an example Process Mode Similar to the batch switch in that all commands supplied with command are executed on each model but in this case the results are not saved and the GUI starts once processing is complete 53 7 The GUI 7 1 Overview Aten s main window is predominantly taken up with the rendering canvas where model s are displayed Multiple models may be displayed simultaneously the current model i e the one to which all editing data operations are send always has a black box drawn around it A single toolbar sits above the canvas providing quick access to file edit and select actions All other functionality is contained wi
307. w empty model called empt ymodel and makes it current model c12 newmodel dodecane creates a new empty model called dodecane makes it current and stores a reference to it in the variable c12 nextmodel Syntax model nextmodel Skips to the next loaded model makes it current and returns a reference to it For example model next nextmodel parentmodel Syntax void parentmodel Makes the parent model of the current trajectory frame the current model For example parentmodel prevmodel Syntax model prevmodel Skips to the previous loaded model makes it current and returns a reference to it 213 For example model prev prevmodel savemodel Syntax int savemodel string format string filename Save the current model in the format given which should correspond to a model export Filter nickname to the filename specified If the save was successful an integer value of 1 is returned otherwise 0 For example int success savemodel xyz home foo newcoords test config saves the current model in xyz format to the filename given setname Syntax void setname string name Sets the name of the current model For example setname panther gives the current model the cool sounding name of panther Ahem showall Syntax void showall Makes any previously hidden atoms in the model v
308. xportmap 171 clearexpression 171 clearlabels 196 clearmap 171 clearmeasurements 200 clearpatterns 217 clearpoints 155 clearselectedbonds 138 cleartrajectory 249 contains 242 converge 205 copy 159 cos 197 createatoms 209 createexpression 172 createpatterns 217 currentatom 131 currentmodel 209 currentpattern 217 cut 159 debug 246 delete 159 deleteff 172 deletemodel 210 deselect 230 deselectf 231 deselectfor 231 deselecttype 231 disorder 158 334 do 165 dotproduct 197 ecut 161 elec 161 endchain 142 eof 219 equivalents 172 error 203 exp 197 expand 232 exportmap 172 ffmodel 173 ffpattern 173 filterfilename 220 finaliseff 173 finalisegrid 187 finalisemodel 210 find 220 firstframe 249 firstmodel 210 fix 131 fixtype 174 flipx 252 flipy 252 flipz 253 fold 149 foldmolecules 149 for 165 frameenergy 161 frameforces 180 free 132 ftoa 243 geometry 200 getatom 132 getcombinationrule 174 getenv 246 getenvf 246 getenvi 247 getff 175 getline 220 getmodel 211 getpattern 218 getsite 239 getview 258 glyphatomf 182 glyphatomr 182 glyphatomsf 183 glyphatomsr 183 glyphatomsy 183 glyphatomv 182 glyphcolour 184 glyphdata 184 335 glyphsolid 184 glyphtext 185 gridalpha 188 gridaxes 188 gridcolourprimary 188 gridcolourscale 189 gridcoloursecondary 189 gridcubic 189 gridcutoff 190 gridcutoffsecon
309. y commas such delimited data can be read in more easily In such cases it is not necessary to know beforehand the number of characters taken up by each item on the line since the delimiters separate adjacent data items A simplified method for reading and writing can be employed in these cases Commands providing delimited reading and writing are Table 11 8 Delimited read write commands Command Function readline Read delimited items from a source file placing into the variables provided readnext Read the next delimited item from a source file placing into the variable provided readvar Read delimited items from a source variable placing into the variables provided writeline Write the supplied items to a single line in the output file separating them with whitespace writevar Write the supplied items to a supplied string variable separating them with whitespace Note that all are called the same as their formatted counterparts but minus the f at the end of the name Delimited Data Example Consider this example datafile Na 0 0 IEO 0 0 al O 0 0 0 0 Na 0 0 O 0 0 286 Since the data items element type and coordinates are separated by whitespace we need only provide the target variables to the relevant command a formatting string as is demanded by the printf command is not required Using the readline command the following code will parse this data correctly double x y 2Z string el while eof readline e
310. y az and the origin getview Syntax void getview Outputs the rotation matrix elements and position vector of the camera for the current model The list of numbers may be passed directly to the setview command to re create the view exactly For example getview orthographic Syntax void orthographic Set the view for all models to be an orthographic projection For example orthographic perspective Syntax void perspective Set the view for all models to be a perspective projection 258 For example perspective resetview Syntax void resetview Resets the view rotation and zoom for the current model For example resetview rotateview Syntax void rotateview double rotx double roty Rotates the current view by rotx degrees around the x axis and roty degrees around the y axis For example rotateview 10 0 0 0 setview Syntax void setview double ax double ay double az double bx double by double bz double cx double cy double cz double x double y double z Sets the rotation matrix and position vector of the camera for the current model The output of getview can be passed to setview to recreate an existing camera rotation and position For example serview ki O 50 0 I 0 l 060 00 10 0 sets a view with the z axis pointing up and the y axis normal to the screen 1 e rotated 9
311. y double Position y component rz double Position z component selected int Whether the atom is selected 1 or unselected 0 style string The current Drawing Style of the atom see Section 16 7 symbol string Element symbol of the atom type ffatom Forcefield type of the atom v vector Velocity vector vx double Velocity x component vy double Velocity y component vz double Velocity z component Z int Atomic number of the atom 8 2 5 Atom Type Functions findbond Syntax bond findbond atom i Return the bond if any between this and the and specified atom i 8 2 6 BasisPrimitive Type The basisprimitive type provides access to basis primitive coefficient and exponent information in a basis shell Table 8 4 BasisPrimitive Type Members Member Type RW Description exponent double Exponent of the basis primitive coefficients double Coefficients of the basis primitive 8 2 7 BasisPrimitive Type Functions addcoefficient Syntax void addcoefficient double coeff 102 Add a new coefficient to the basis primitive 8 2 8 BasisShell Type The basisshel1 type contains information about a basis shell centred on a specific atom in a model allowing a full basis set specification to be associated with a system Table 8 5 BasisShell Type Members Member Type RW Description atomid int Atom ID on which the basis shell is centred nprimitives int Number of primitives defined for t
312. y one point The parent group does not need to be created beforehand if the named group does not currently exist it will be created Note that the group widget itself is not visible and so many contain any number of radio buttons spread over many tabs and pages radiogroup None A radio group is a collection of radio buttons of which only one can be selected at any one time A radiogroup only provides the means to collect a set of radio buttons together and it not itself visible The index of the selected item is returned stringradiogroup None Same as radiogroup except that the text label of the selected item is returned Option Layout The layout of specified GUI controls is done in as simplistic a manner as possible while still offering reasonable control over the positioning of elements If no layout options are specified all defined controls will be added one after the other in a single row left to right possibly stretching further than the screen can handle At the very least the newline command should be used to force a control option to start a new row of controls in the GUI All controls are added into a grid Qt s QGridLayout so that controls always line up nicely It is also possible to group controls together in tabbed widgets and group boxes All controls except the plain label are two units wide on the grid and this should be borne in mind when stretching a single control to be the same width as a set
313. y pdens into the current model newgrid Syntax grid newgrid string name Creates a new empty grid with the provided name in the current model and returns a reference to it For example grid g newgrid charlie creates a new grid called for some reason charlie 193 9 15 Image Commands Save bitmap and vector images of the current view The GUI is not required in order to save images using these commands from the command line for example works just as well models still have a current view even without the GUI and can be rotated translated etc just as if they were in the GUD savebitmap Syntax void savebitmap string format string filename void savebitmap string format string filename int width int height void savebitmap string format string filename int width int height int quality Saves the current view as a bitmap image Allowable values for format are Table 9 2 Bitmap Formats Format Description bmp Windows Bitmap jpg Joint Photographic Experts Group png Portable Network Graphics ppm Portable Pixmap xbm X11 Bitmap xpm X11 Pixmap If width and height are not specified the current dimensions of the view are used 800x600 if no GUL is present The quality option determines the compression used on saved images affecting for example the quality and size of jpegs and pngs and should be an integer between 1 and 100 with 100 being the best compression
314. yleradius double 4 The atom radii used for selection and rendering in the four Drawing Styles see Section 16 7 backcull int Whether culling of backward facing polygons should be performed backgroundcolour double 4 Background colour of the main canvas on which models are drawn bondstyleradius double 4 The bond radii used for selection and rendering in the four Drawing Styles see Section 16 7 bondtolerance double Tolerance used in automatic calculation of bonds between atoms cachelimit int The trajectory cache size in kilobytes trajectory files calculated to have more than this amount of data will not be cached in memory calculateintra int Controls whether intramolecular contributions to the energy forces are calculated calculatevdw int Controls whether short range Vdw 124 chargelabelformat clipfar clipnear colourscales colourscheme combinationrule commonelements dashedaromatics densityunit depthcue depthfar depthnear distancelabelformat eleccutoff elecmethod encoderargs encoderexe energyunit energyupdate ewaldalpha ewaldkmax ewaldprecision forcerhombohedral framecurrentview framewholeview string double double colourscale 10 string string string int string nt int H int string double string string string double int double int 3 double int int int 125 contributions to the
315. yntax int readvar string source int double string var Parse the contents of the supplied string source into the supplied variables assuming delimited data items Delimited items read from source are converted automatically to the type inferred by the target variable The number of data items parsed successfully is returned For example string data rubbish ignore Carbon green 1 0 2 5 5 3 string element discard vector v int n readvar data discard discard element discard v x v y v z discard printf Element s n i n element n outputs Element Carbon n 7 The character string in the variable data is parsed with delimited chunks placed into the supplied variables Note the repeated use of the variable discard used to get rid of unwanted data Also note that there are not enough items in data to satisfy the final occurrence of discard and so the function returns a value of 7 as opposed to the actual number of target variables supplied 8 readvarf Syntax int readvarf string source string format int double string var Parse the contents of the supplied string source according to the supplied format string placing in the supplied variables The number of format specifiers successfully parsed or to look at it another way the number of the supplied variables that were assigned values is returned For example string a b data abc def123456 0 double d int i n n

Aten v1.7 User Manual Last Updated Thursday, 21 July 2011

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