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RMCProfile User Manual

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1. Csp Csp D 3 148 x Cbz Cpz D 2 155 x Cbz H D 2 472 X Cearb Ocarb D 3 48 fo x Coarb Cbz Csp Cspe D 3 60 fo x Csp H D 2 472 1 X Cim Nim D 8 840 fo x Cim H D 2 208 h x We recommend using realistic rather than artificial potentials provided that the weighting you use for the data is derived from the errors on the data 11 97 RMCProfile Manual v6 4 6 3 1 INTERATOMIC POTENTIALS 3 1 2b Bond angle potentials We use a simple harmonic cosine potential to describe the energy associated with bending of bonds E 5K cos 8 cos bo 3 4 where is the instantaneous bond angle and Ou is the set angle This equation can be expanded to yield E 2K sin 2 sjn 2 as 4K sin bo 0 b0 where the angles are defined in units of radians rather than degrees As with the bond stretching potential we recommend the use of realistic values of the parameter K Values of K sin 6 for some common bonds are units of K are eV and angles are given in degrees Cbz Cpz Cpz K sin 99 39 71 09 120 Cbz Cpz H K sin 09 25 61 6o 120 3 1 3 The main data file Consider the following example from an input dat file POTENTIALS gt STRETCH C C 4 0 eV 1 15 Ang gt STRETCH Zn C 2 0 eV 1 95 Ang gt STRETCH_SEARCH 10 gt ANGLE Zn C C 4 0 eV 90 0 deg 1 95 1 95 Ang gt ANGLE C
2. The PPM format is described at http en wikipedia org wiki Portable_pixmap which is available from http www imagemagick org 16 97 RMCProfile Manual v6 4 6 3 1 INTERATOMIC POTENTIALS Figure 3 1 Example of a stereographic representation of the bond orientation function generated by RMCProfile where the two placeholders indicated by lt name gt denote the main file name and the name of the file you want to generate and lt extension gt gives the file type examples are png gif pdf and eps The modifier transparent black will convert black to transparent the background is written using a black colour and this allows the background to be made transparent If you get an error message of the type convert unable to access configure file colors xml you are probably able to ignore it the message is telling you that it has used an internal colour map Other graphics program such as GraphicConverter for Mac OS X and Adobe s Photoshop are able to read and manipulate files in the PPM format 3 1 6 Converting the histogram file to a PPM file We provide a utility called bondplot a Fortran 90 program to allow you to convert from the histogram file to a PPM file This gives the user some control over various options which have assumed values when the file is generated by RMCProfile You run bondplot as a simple command within the shell or command interface with no parameters The program will in order
3. This restraint defines a configuration of unlinked triangular molecules formed from the second and third atom types in the configuration as the name suggests it was first used for studying the molec ular crystal NaNO3 To use this restraint option 10 needs to be specified in the dat file and poly no and on files supplied The poly file contains a title line which is ignored and the next line must contain the ideal N O bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the angle restraint e 300 The no file contains a list of oxygen neigh bours around each nitrogen atom and the on file contains a list of the nitrogen neighbours around 65 97 RMCProfile Manual v6 4 6 4 7 POLYHEDRAL RESTRAINTS each oxygen atom both of these files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 11 The KCN restraint This restraint defines a configuration of unlinked binary molecules formed from the second and third atom types in the configuration as the name suggests it was first used for studying the molecular crystal potassium cyanide To use this restraint option 11 needs to be specified in the dar file and poly cn and nc files supplied The poly file contains a title line which is ignored and the next line must contain the ideal CN bond distance to be used and the weighting for this bond restraint e 100 The c
4. L Goodwin M G Tucker M T Dove and D A Keen Phonons from powder diffraction A quantitative model independent evaluation A L Goodwin M G Tucker M T Dove and D A Keen Physical Review Letters 93 art no 075502 4 pp 2004 Erratum Phonons from powder diffraction A quantitative model independent evaluation Phys Rev Lett 93 075502 2004 Physical Review Letters 95 art no 119901 4 pp 2005 13 S A Wells M T Dove and M G Tucker Reverse Monte Carlo with geometric analysis RMC GA Journal of Applied Crystallography 27 546 544 2004 14 Q Hui M G Tucker M T Dove S A Wells and D A Keen Total scattering and reverse Monte Carlo study of the 105 K displacive phase transition in strontium titanate Journal of Physics Condensed Matter 17 S111 S124 2005 15 M G Tucker A L Goodwin M T Dove D A Keen S A Wells and J S O Evans Negative thermal expansion in ZrW20g Mechanisms rigid unit modes and neutron total scattering Physical Review Letters 95 art no 255501 4 pp 2005 16 M G Tucker DA Keen J S O Evans and M T Dove Local structure in ZrW20g from neutron total scattering Journal of Physics Condensed Matter 19 art no 335215 16 pp 2007 17 A L Goodwin M G Tucker M T Dove E R Cope and D A Keen Model independent extraction of dynamical information from powder diffraction data Physical Review B 72 art no 214304 15 pp 2005 18 A L G
5. agn file contains a list of the nitrogren neighbours around each silver atom All of these neighbour files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 13 The Zn CN p gt restraint This restraint defines a network of linked tetrahedra formed from the first three atoms in the con figuration as the name suggests it was first used for phases of zinc cyanide This differs from the SiOz restraint in that the network consist of tetrahedra link by two bridge atoms in this case carbon and nitrogen with zinc at the centre of the tetrahedra To use this restraint option 13 needs to be specified in the dat file and poly zncn czn nzn cn and nc files supplied The poly file contains a title line which is ignored and the next line must contain the ideal Zn C bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the tetrahedral angle restraint e 300 The following line must contain the ideal CN bond distance to be used and the weighting for this bond restraint The next line must contain the ideal N Zn bond distance to be used and the weighting for this bond restraint The zncn file contains a list of carbon and nitrogren neighbours around each zinc atom the czn file contains a list of the zinc neighbours around each carbon atom and the nzn file contains a list of the zinc neighbours around each nitrogen atom The cn file co
6. distances between pairs of atoms Default val ues are zero if this keyword is not provided Currently the units are not interpreted default units are Angstroms 30 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES NEUTRON_COEFFICIENTS Requires list of neutron scattering coefficients products of scattering lengths and number concentrations for all atom pairs The data are allowed to straddle several lines of the file De fault units are 1079 m The default values are calculated by the code if this keyword is not given It can be overwritten within the neutron data block of subordinate keywords see sec tion 4 1 6 z EUTRON_REAL_SPACE_DATA Introduces a block of data concerning a set of neutron derived real space data i e a pair dis tribution function weighted by the neutron scat tering lengths Text can follow the but will be ignored This keyword must be followed by a block of subordinate keywords Do not provide if you have no neutron real space data NEUTRON RECIPROCAL SPACE DATA Introduces a block of data concerning a set of neutron scattering data Text can follow the but will be ignored This keyword must be fol lowed by a block of subordinate keywords Do not provide if you have no neutron reciprocal space data NUMBER_DENSITY Requires the value of the number density should you want to over ride the value in the configuration file Default units are A 7
7. t appreciated that they weren t completed Written the ability to read his6f files not having done this before was an oversight Some small rearrangements with the storage of variables to make coding easier Some new subroutines and one new file exists which are not used by v6 3 3 but which will be used by v6 4 and put them in here because am aiming at editing my development version only when possible v6 3 1 1 The headline change is that it reads and writes rmcf6f configuration files This may now sound like a big deal but took quite a bit of programming to get there have added a number of new subroutines to make this work have the undocumented option to resort the configuration but this doesn t quite work so will fix it soon one of the planned tweaks You don t need to use this tool with the example configuration It will use the keyword SORT in the input file think it is an easy fix to make but want to start getting the testing of the RMC procedure working The program now creates csv files for the partial g r and partial S Q functions with head ers that tell you which partials you have also put headers into the out files It has long been a pet dislike of mine that you have to deduce which column refers to which partial from external information so am pleased to have fixed this one think that the code still generates a cfg file when you don t want one so nee
8. where you can run scientific codes rather more easily 84 97 RMCProfile Manual v6 4 6 CHAPTER 6 EXAMPLES Chapter 6 Examples 6 1 Overview RMCProfile comes with a directory of example files each example consists of a folder containing the folders gsas data and rmc The aim is to supply all the information required to get RMCProfile running on the example system The gsas folder has the GSAS refinement and data to provide all the Bragg profile information it also includes a cfgcom file containing the information to produce a starting configuration with the crystal program The data folder contains time of flight neutron structure factor F Q and radial distribution g r data These two folders provide all the information required to run RMCProfile and produce a configuration of the system The rmc folder contains a completed run and all the output files illustrate what the result will hopefully look like and for you to modify to help run RMCProfile on your own data 6 2 Example 1 GE SFe is a disordered molecular crystal made up of SF octahedra arranged over the crystal lattice Molecular crystals are often the most disordered crystalline systems and as can be seen from plotting the example data often show a large amount of diffuse scattering The example data and files supplied are from the GEM diffractometer at ISIS and were collected at 190K At this temperature the crystal structure has body centred cubic symmetry with one mo
9. 00 0 9269717E 02 0 0000000E 00 0 3000000E 01 0 0000000E 00 0 0000000E 00 0 5000000E 01 0 0000000E 00 0 0000000E 00 0 8900000E 00 0 4750513E 00 0 1049418E 02 0 9100000E 00 0 4789928E 00 0 1090569E 02 0 9300000E 00 0 4766961E 00 0 1046322E 02 0 9500000E 00 0 4731495E 00 0 1022877E 02 0 9700000E 00 0 4702018E 00 0 9821923E 03 SUC eis The lines beginning with the are treated as comments but the third comment line is important because it contains the start and end point numbers that are read 4 4 Bragg scattering The ability of RMCProfile to handle separately the information from Bragg scattering enables the RMC simulation to reproduce the spatial distribution of atom positions The program uses a Rietveld like approach in that it fits the Bragg peaks in the diffraction profile using background and 54 97 RMCProfile Manual v6 4 6 4 4 BRAGG SCATTERING lineshape functions obtained from the GSAS programit and adjusts the configuration to match the intensities of the Bragg peaks 4 4 1 The essential data files The information that is required to control the Bragg fitting was described in the section on the Version 6 data file above We remark here that the configuration is a supercell of the crystal unit cell of relative size Ny x Ny x Nz The gt SUPERCELL line within the BRAGG keyword block contains the three integers Nx Ny Nz When we now consider the Miller indices hA k these refer to the fundamental un
10. 3 Generated files RMCProfile automatically generates two files namely a amp file and one called hkls These are used for subsequent restarts and the user need not be concerned with the details In principle you might expect not to have to give this information since it is easily computed In a future version we will remove the need for this parameter 56 97 RMCProfile Manual v6 4 6 4 5 RMCPROFILE VERSION 3 FILES 4 5 RMCProfile version 3 classic files In this section we describe the input files required when running RMCProfile in the version 3 classic mode Unless you like to work harder than you need to we can t find any obvious reason to recommend this approach in preference to the new version 6 approach described previously If you find this daunting which one of the authors does then skip past this to the next chapter 4 5 1 The dat file This is main control file from here everything you want RMCProfile to do is defined An example is given below the text after the explains what that line is for SF6_at_190K 0 0685951 number density 4 0 1 2 1 8 cut offs OH Or maximum move 0 020 r spacing false whether to use moveout option false collect configurations 1000 step for printing 2400 60 Time limit step for saving 3 0 No of g r neutron X ray sf6_190k gr 1500 0 0 00165 03942 23486 0 05 false sf6190kbankliconv29p42rmc dat 1 3000 D 0
11. 6 INPUT FILES VW WM WM WM VV WM WM NEUTRON_RECIPROCAL_SPACE_DATA gt gt DATA_TYPE VW WM WM WM VV WM WM CML gt FILENAME ag3cocn6_300k_tr dat DATA_TYPE T r FIT_TYPE D r START_POINT 1 END_POINT 2000 CONSTANT_OFFSET 0 0 WEIGHT 0 02 NO_FITTED_OFFSET 1 ag3cocn6_300k_sq dat S Q Qi Q FILENAME FIT_TYPE START_POINT 1 END_POINT 2471 CONSTANT_OFFSET WEIGHT 05 NO_FITTED_OFFSET NO_FITTED_SCALE CONVOLVE 0 0 CCVIZ CCviz FLAGS gt gt gt gt NO_MOVEOUT SAVE_CONF IGURATIONS NO_RESOLUTION_CONVOLUTION CSSR BRAGG Vv BRAGG_SHAPE RECALCULATE SUPERCELL WEIGHT gsas2 6 4 6 0 01 POTENTIALS gt VW WM WM WM VV WM WM END STRETCH STRETCH STRETCH STRETCH_SEARCH ANGLE Ag NN ANGLE Co CC ANGLE_SEARCH TEMPERATURE PLOT C N 8 5 eV 1 15 Ang Co C 5 0 eV 2 0 Ang Ag N 6 0 eV 1 5 Ang 20 10 eV 180 deg 1 5 1 5 Ang 10 ev 90 deg 1 8 1 8 Ang 10 deg 300 K 400 pixels colour charcoal zangle 90 0 zrotation 45 0 deg 42 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES This file is hopefully self explanatory in light of the keyword descriptions above but some points might help 1 An extensive set of metadata is provided below the initial two comment lines Although none of these lines are essential they will provide the user with a good source of information when returning to the input or output
12. Default value is the the value in the configuration file if this keyword is not provided PHASE Requires text to act as a description of the phase for the material being studied For ex ample if you are studying quartz you can de fine whether this is the low temperature or high temperature phase This is used for metadata and is not compulsory PRINT_PERIOD Requires number of steps between printing to the log file POLYHEDRAL_RESTRAINT Requires the number label of the polyhedral constraint see the main manual Default is to not use this constraint if this keyword is not pro vided 31 97 RMCProfile Manual v6 4 6 POTENTIALS PRESSURE R SPACING RMC_NOTE SAVE_CONF IGURAT ION_FORMAT SAVE_PERIOD SORT_ATOMS SWAP H EMPERATURE TIME_LIMIT TITLE 4 1 RMCPROFILE VERSION 6 INPUT FILES Introduces a block of data concerning the use of interatomic potentials See Default is to not use this constraint if this keyword is not pro vided Use of this keyword means that use of the POLYHEDRAL_RESTRAINT keyword is ignored because the two keywords provide ac cess to similar functionality See page 10 Requires text to denote the pressure of the ma terial being studied This is used for metadata and is not compulsory Units are not parsed as such Requires the value of the spacing used in the pair distribution functions Current
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14. Zn C 2 0 eV 180 0 deg 1 95 1 15 Ang gt ANGLE_SEARCH 10 deg gt TEMPERATURE 300 K gt PLOT pixels 400 colour charcoal zangle 90 0 zrotation 45 0 deg Here we have defined two bonds for C C and Zn C bonds which are given in the gt STRETCH lines The order in which the information on the two bonds is provided will lead to the as sociation of numbers 1 and 2 to the two bonds which you need to know about for the bonds file below Here we have requested that RMCProfile search for bonds of distance 1 15 and 1 95 A respectively with a tolerance of 10 We could have specified the tolerance in absolute units instead The example from which this snippet was taken consisted of ZnCg octahedra We have therefore defined a bond bending potential the first gt ANGLE line to describe the C Zn C angle of 12 97 RMCProfile Manual v6 4 6 3 1 INTERATOMIC POTENTIALS equilibrium value 90 The octahedra are connected via C C bonds which form part of a linear Zn C C Zn linkage We might want to add a potential to ensure the RMC simulation doesn t allow large departures from this linear configuration and this is the role of the second angle constraint Note that the equilibrium angle is actually used in the initial search of atom triplets and the tolerance on the angles for the initial search is provided by the ANGLE_SEARCH 10 line As with the bond stretching potential the ordering in which
15. accurate The line of dots is used to divide the header from the data So now we consider the actual bonds data For each bond there is a list of all the atoms in the same order as the configuration if you break this order that will be recognised and the program will abort We look at the data on any one line and consider the following example line Jk Zon 2 Ss 3 C7 4C 7 6C 7 10 C7 4 The first number specifies the atom number in the configuration file and this is followed by the chemical element symbol The third number gives the bond number So in this example we are looking at the first atom in the configuration which happens to be a zinc atom and this lines is concerned with the second bond specified in the input file The double colons are important because they separate the description of the data to the left from the actual bond data on the right Consider first the last number This gives the number of bonds which in this case is 4 denoting a tetrahedral coordination Note that there are four semicolons these separate the data for each bond And the data for each bond merely consists of an atom number and its chemical symbol So in this example the zinc atom is bonded to four carbon atoms which are numbers 3 4 6 and 10 in the configuration Ideally you should not need to edit this file but if something in your system is more complicated then sadly you will have to do some hand work 3 1 5 The triplets file The
16. block of data keywords where required you might not bother for the data sets using the natural isotopes 4 1 7 Data normalisations One unfortunate aspect of the world of total scattering is that different communities have developed different terminologies and definitions Our colleague David Keen did us a great service by publish ing a comparative review of these and we recommend that you keep a copy of this paper beside you RMCProfile will accept and work with several of the conventions and definitions used for total scattering and PDF functions Here we review the key equations that RMCProfile supports 4 1 7a The pair distribution function We start with the basic definition of the partial PDF namely that the number of atoms of type lying within a shell of radius r and thickness dr centred on an atom of type is given as Arr pigi r dr where or is the number of atoms of type j per unit volume We have the following limiting cases gi r 0 0 Qi r gt o0 1 4 1 It will be convenient to introduce the number concentration cj where o cjp where p is the total number of atoms per unit volume Clearly c 1 We define an overall PDF by merging all the partial PDFs with appropriate weighting consistent with the concentration and neutron scattering power as G r E ciC bibj gilr Z 1 4 2 ij where 6 is the scattering factor of atom type j The limiting values are 2 G r 0 x ob G r c 0 4
17. dat file above the first and second atom types have been specified however since the probability is set to zero this line is not required but given by way of example Typically RMCProfile just translates a single atom during each Monte Carlo step however for systems with site disorder such as cation ordering or vacancies this is not completely suitable So a swap move enables RMCProfile to switch the position of one atom with another during a Monte Carlo step The balance between how many swap moves and then how many translations are required to relax the surrounding structure is non trivial So with RMCProfile there are two approaches the first is trial and error by just setting the swap probability probably the most common option the second option is to set the autotuning to true This will then try to alter the swap move probability to maintain an appropriate level of accepted moves 4 5 2 The cfg file The cfg file contains the information about the supercell of atoms RMCProfile will use to fit the data This file together with the dat file are the minimum required files RMCProfile can be run without data but not without a configuration of atoms to move The format of this file is the same as with RMCA and consists of some header information about the number of atoms the configuration dimensions the atom types and then a list of the atomic positions in fractional coordinates from 1 to 1 The order of the information and indeed the ov
18. describes the distribution of interatomic distances G r A Cmenbmbn Gmnlr 1 7 8 m n and p is the number of atoms of any type per unit volume The individual pair distribution functions are defined as Nmn r 7 Aart pmdr 79 Gent where Nmn r is the number of atoms of type n lying within the range of distances between r and r dr from any atom of type m and pm Cmpo It is common to define the pair distribution function in terms of the new function D r 4rrpo G r 7 10 so that Qi Q D r sin Qr dr 7 11 The reverse transformation is then given as D r di Qi Q sin Qr dr 7 12 Wright 1993 1994 1997 Chieux 1978 Dove 2002 This transform provides the means by which the information about structure over short length scales as encapsulated in the function D r can be extracted from the experimental measurements The experimental task Wright 1993 1994 1997 is to obtain the best measurements of Qi Q from the total scattering data It is not within the purpose of this Appendix to explain the experimental de tails these have been documented elsewhere Wright 1993 Howe et al 1989 Dove et al 2002 However it is essential to appreciate that it is important to determine OO to a high value of Q typically of order 30 50 A in order to achieve the best possible resolution in D r the resolution Ar is given as 27 Qmax Where Qmax is the maximum value of Q achieved in the measureme
19. displacement moves of magnetic species affect the nuclear scattering functions Conse quently the only significant additional computational cost suffered is involved in the translations of magnetic atoms whereupon changes in both nuclear and magnetic scattering functions must be calculated 3 2 2 Algorithm Spin orientation moves are implemented within RMCProfile as follows The orientation of each spin i e the normalised spin vector is treated as a point P on the surface of a sphere A random spin move vector M whose magnitude omax determines the maximum change in spin orientation and is determined by the user is added to P and the resultant vector projected back onto the surface of the sphere to give the new spin orientation P The probability distribution associated with this algorithm has its maximum at a move size of omax and so it is usually appropriate to limit the size of this parameter to relatively modest values ca 0 1 The magnetic contribution Smag Q to the scattering factor is calculated from the RMC configura tions via two real space correlation functions Air and B r 2 ey S ery i Smag Q aM SIE 4T pCM o sin Qr Sin Or cos Or oe far a BUN K one har 3 6 18 97 RMCProfile Manual v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING where Cy is the concentration of the relevant magnetic specices p is the number density of magnetic atoms e y Me and c carry their usual meanings gJ is the magnetic mom
20. file The main whatever dat file which is the file that controls the RMC simulation is designed to be both flexible and readable The format is simple and has just a couple of basic rules These are illustrated in the following example o RMC refinement of Ag3Co CN 6 TITLE Ag3CoCN6_300K MATERIAL Ag3 Co CN 6 NUMBER_DENSITY 0 052612 NUMBER ANG 3 MAXIMUM_MOVES 0 0149 0 0200 0 0445 0 0411 ANG R_SPACING 0 020 ANG PRINT_PERIOD 10000 STEPS TIME LIMIT 0 0 MINUTES SAVE_PERIOD 0 0 MINUTES ATOMS Ag Co C N NEUTRON_REAL_SPACE_DATA 1 27 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES gt FILENAME ag3cocn6_300k_tr dat gt START _POINT 1 gt END POINT 2000 gt WEIGHT 0 02 FLAGS gt SAVE_CONFIGURATIONS END You immediately notice the first main rule namely the use of 2 and gt symbols These are used to define the type of data Anything after these characters is treated as a comment on that line Having this character on a line indicates that the line is a keyword that is it defines the type of data about to be provided There are three main cases a where the keyword stands alone eg END You still need the symbol in the major keywords in this case in order for the parser to work we will see an exception with the subordinate keywords b
21. files These data are reproduced within the CML file 2 The atom list here is for the example Ag3Co CN g where the configuration file orders the atoms within an initial block of all the Ag atoms first followed by all the Co C and N atoms in blocks 3 This example is using one file of neutron T r data and one file of neutron S Q data The example is providing the request that a different representation of the data are used in the fitting 4 No neutron coefficients are provided these will be calculated from the internal table of atomic scattering lengths and the computed number concentrations 5 The CML line without subordinate keywords leads to the production of a report CML file that does not contain the configuration and the input and output configurations are in standard format 6 The dataset includes a Bragg profile fitted with the gsas2 profile shape The RMC configura tion is specified to be a 6x 4x6 supercell of the unit cell The indexing of the Bragg reflections is to be recalculated 4 1 6 Neutron coefficients The neutron coefficients are defined as fj cjcjb bj where i and j label two atom types c is the number concentration of atom type i and b is the coherent scattering length of atom type i This is illustrated with the example of Ag3Co CN g The atoms in the configuration are ordered as Ag Co C and N The corresponding values of c are 46 146 Die and Die respectively The coherent scattering lengths f
22. in this file correspond to a logarithmic probability of observing a spin pointing in a specific direction An intuitive method of viewing these distributions is a projection onto the surface of a sphere There is a program provided that converts mno_spins out into a sphere projection we execute it with the command 24 97 RMCProfile Manual v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING spinplot lt spinplot in This produces a picture in the ppm format which we convert using convert mno_spins ppm mno_spins bmp A typical distribution is shown in Fig 3 7 which in this case shows that the spins are aligned parallel and antiparallel to an axis very close to 112 N Figure 3 7 A typical spherical spin distribution black low probability white high probability The view is taken looking down 100 with the 010 axis to the right hand side and the 001 axis towards the top of the figure In this particular case alignment appears to be approximately parallel and antiparallel to 112 We can use the same program to look at this distribution from arbitrary angles and even produce an animated gif We will do this quickly here by editing the file spinplot in changing the last entry from F to T This part of the file is a flag that instructs the program to prepare a series of views that can be assembled to form an animation Re running the command spinplot lt spinplot in will now give a series of 24 files numbered 01 mno_s
23. magnetic structure of the well known antiferro magnet MnO At temperatures below 120K the S 3 magnetic moments of the Mn ions align ferromagnetically within 111 planes of the rocksalt crystal lattice The magnetisation direction within planes then reverses from one plane to the next giving the overall antiferromagnetic struc ture shown in Fig 3 2 In fact there is also a slight deviation from cubic lattice symmetry associated with this magnetic transition but here we will ignore this effect The MnO atom and spin RMC configurations We are going to refine the spin orientations in a 4 x 4 x 4 supercell of the unit cell shown in Fig 3 2 The file mno cfg contains the positions of 512 atoms 256 Mn and 256 O atoms The positions of these atoms have been displaced slightly from their average positions A version of this configuration file in the format readable by ATOMEYE is given as mnoeye cfg It is worth taking a look at the structure in ATOMEYE at this stage just to familiarise oneself with the atom positions A picture of the configuration is shown in Fig 3 3 A set of 256 random spin orientations are given in the file mno_spin cfg One method of vi sualising these orientations is to colour the Mn atoms in our ATOMEYE configuration according to the individual spin directions There is a program ATOMEYEPREP provided that helps prepare the relevant files If we run the command atomeyeprep lt atomeyeprep in 20 97 RMCProfile Manua
24. radial distributions to a distance of the minimum box edge divided by two so very different box edges will just produce wasted information The next three lines contain the unit cell parameters in vector form Again for a cubic system or indeed any orthogonal system this is very straightforward with the diagonal of the matrix be ing a b and c respectively For non orthogonal systems this is not so straightforward and the lattice_vectors program supplied with RMCP rofile can be used to produce the vectors in the correct format for the crystal program The next line contains the number of different atom types For each atom type the subsequent lines then define the number of atoms of that time in the unit cell and then the fractional coordinates between 0 and 1 for each atom In the example shown there are two sulphur atoms and then 12 fluorine atoms The following line contains a zero which defines the number of Euler angles is now an obsolete throwback to a time when the crystal program was used for molecular systems The final line contains the name of the file to which you wish the configuration to be written And yes you have to work all these numbers out for yourself by hand and then type them in or else you can write a program to generate them yourself but the extra step to create the configuration is so trivial that you might as well do it all yourself The crystal program is run in a command prompt window in two ways The simples
25. the information on the two bond angles is provided with lead to the association of numbers 1 and 2 to the two triplets which you need to know about for the triplets file below In the first case we have requested that RMCProfile search for bond angle triplets with bond lengths of distance 1 95 A for both Zn C bonds with a tolerance of 10 on the bond lengths and with a tolerance of 10 on the bond angle We could have specified the tolerance on the bond angle in terms of a percentage instead The temperature provided plays a role that is related to weighting of the data and in the polyhedral restraints method this is seen as a parameter to tune in concert with the weighting on the data However when using realistic numbers in the interatomic potentials the sample temperature should be able to play a quantitative role in the modelling at least for the D parameter in that it should give rise to a peak in the PDF of correct width The exact value of r can be tuned to correspond with the position of the peak in the PDF which may not exactly match the recommendations The gt PLOT line enables the bond orientation distribution function to be plotted as a coloured stereographic projection this is discussed below 3 1 4 The bonds file The bonds file will be generated by the first run of RMCProfile using the information contained within the POTENTIALS keyword block and will have the root name of the s
26. triplets file which contains the information about bond angles will have the root name of the simulation with the triplets extension As with the bonds file the triplets file is created automatically if it doesn t exist A typical example has the form Metadata file type Bonds file for RMC simulation Metadata creation date 12 08 2009 Metadata material ZncC4 The lt snip gt lines replace similar data removed for the sake of brevity 14 97 RMCProfile Manual v6 4 6 3 1 INTERATOMIC POTENTIALS atoms 10 bonds 2 triplets 2 Number o Number o FH FH Fh Number o Sp 1 33 101 C 102 C 101 103 G 7 101 C 104 C 101 105 G 7 4 Zn 1 0 lt snip gt LD C Ll se 0 101 C 1 Zn 102 C 1 Zn 103 C 1 Zn 104 C 1 Zn 105 C 4 lt snip gt TOL C 2 zs 1 Zn 201 C 1 HOT C 2 ee HIT C2 Zn o 1 lt snip gt First we note that this file will be generated automatically by RMCProfile at the first run when the POTENTIALS keyword block is used Thereafter its existence will be recognised and the data within the file will supersede the triplets data provided in the input file This is a good thing since often the bonds are established on a nicely ordered structure with no fluctuations that are hard for an automatic method to detect If you don t want to use an existing triplets file then rename or delete it The structure of this file is import
27. use ATOMEYE for this purpose so we need to run the command atomeyeprep lt atomeyeprep in which will produce a new mnoeye clr file from the equilibrium spin configuration Launching ATOMEYE with atomeye bat mnoeye cfg will now show the new structure Because there are four different symmetry equivalent 111 axes the actual direction of the magnetic ordering will differ from run to run Also the absolute direction of the spins will vary as well and so the colours may also be different Nevertheless a typical con figuration is shown in Fig 3 6 What should be clear after some playing with the orientation is that the magnetic structure is now composed of ferromagnetic layers as described in the introduction X mnoeye SET gt A Figure 3 6 A typical RMC equilibrium configuration as seen in ATOMEYE Finally we return to the series of equilibrium configurations produced by RMCProfile If fewer than 50 configurations have been prepared in the 10 minutes then run the program once again it will automatically resume its sequential numbering from the correct point until sufficiently many have been saved We are going to use these configurations to look at the actual distribution of spin orientations rather than the broad ordering pattern which we observed with ATOMEYE To do so we extract a distribution histogram using the command spindist lt spindist in which produces a new file namely mno_spins out The numbers
28. where p is a probability distribution function and for a harmonic crystal it is a simple Gaussian function Willis amp Pryor 1975 with a Fourier transform i e the term in the integral that is also a Gaussian The objective of total scattering experiments is to determine the distribution of interatomic distances Indeed the atomic structures of fluids and glasses can only reasonably be described in terms of the interatomic distances Since fluids and glasses are isotropic the scattering function is independent of the direction of Q The scattering function is therefore better described by averaging over all orientations of Q leading to 7 5 This result is derived in Appendix B It is useful to recast the formalism in terms of the distribution of interatomic positions rather than as a sum over all pairs of atoms First we subtract out the terms where j k to give KQ i Q H emb3 7 6 where the first term will describe pairs of atoms and will be considered in more detail below and where Cm is the proportion of atoms of type m Vin Cm 1 The first term can be written as Note that RMCProfile treats the functions i Q and F Q as synonymous the program authors have the bad habit of using both interchangeably in their publications but that reflects that they are individuals after all 89 97 RMCProfile Manual v6 4 6 7 1 TOTAL SCATTERING he S D sin Qr OQ By H Area dr 7 7 where the new function G r
29. will be generated in subsequent writes of the configuration file The Lattice vectors Ang line and the following three lines containing the vectors describing the shape and dimensions of the configuration These lines are not required if 49 97 RMCProfile Manual v6 4 6 4 2 RMC VERSION 6 FORMAT CONFIGURATION FILES you include the Cell Ang deg line but will take precedence if both are included If these data are not include they will be generated by RMCProfile in subsequent writes of the configuration file 9 The Atoms line is required It must precede the block of lines containing the information about each atom 10 The supercell line is not required but is generated by data2config and its inclusion means that it is not required within the main dat file 11 Each atom line follows the format with the following data a An optional number can be provided before the atom symbol to label the atom within the configuration b The atomic element symbol compulsory This requirement is different from Version 3 classic configuration files which do not contain any information about the atom types The advantage of containing this information is that it makes the file self contained you can run analysis programs without needing to obtain this information from other sources This element must be one of the real elements You are allowed to use D for deuterium and you can use Va for a vacan
30. working directory which is associated within your PATH If the program is in your working directory but your PATH is not set up to detect programs within it you need to modify the command to rmcprofile KCN gt KCN log Otherwise you need to give the full name of the program file including all the directory information 2 2 3 Output files RMCProfile will generate a number of output files These include following the KCN example KCN out contains a lot of summary information and generated data 8 97 RMCProfile Manual v6 4 6 2 2 RUNNING RMCPROFILE KCN xml contains a lot of summary information and generated data if you have specified a request for CML data KCN xhtml contains a nice web page summary of the results of the RMC simulation provided you have requested CML data and the use of the ccviz program KCN his6f or KCN his6c contains the configuration and the pair distribution functions generated by the run KCN rmc6f or KCN rmc 6c will contain an updated configuration If you request periodic saves of the configurations these will have a number appended as for example KCN_23 rmc6f KCN_SQpartials csv will contain the calculated partial scattering functions in CSV format KCN SOL os will contain the calculated and experimental data for the first file of scattering data in CSV format If more than one file of scattering data is used the number 1 will be replaced by the subsequent number of the data set
31. 0 0 000000 0 000000 0 000000 11 360000 Atoms 1 Na 0 000000 0 000000 0 000000 1 0 0 0 2 Na 2 840000 2 840000 0 000000 2 0 0 0 3 Na 2 840000 0 000000 2 840000 3 0 0 0 4 Na 0 000000 2 840000 2 840000 4 0 0 0 5 Na 0 000000 0 000000 5 680000 1 0 0 1 6 Na 2 840000 2 840000 5 680000 2 0 0 1 58 Gl 5 680000 8 520000 0 000000 6 1 1 0 59 Gi 5 680000 5 680000 2 840000 7 1 1 0 60 Gl 8 520000 8 520000 2 840000 8 1 1 0 61 Gl 8 520000 5 680000 5 680000 5 1 1 1 62 Gl 5 680000 8 520000 5 680000 6 1 1 1 63 Gi 5 680000 5 680000 8 520000 7 1 1 1 64 G1 8 520000 8 520000 8 520000 8 1 1 d The explanation of the Version 4f format should be sufficient to describe most of the features of this file format with only a few exceptions 1 The first line must contain the phrase Version 6c 2 Here the Lattice vectors Ang set of lines is required and the Cell Ang deg line is both optional and not used by RMCProfile but will be generated in successive writes of the configuration file 3 It stands to reason that the coordinates in the atom lines are now in Cartesian form with units of A It will be assumed that Version 6c configuration files will have names with a rmc6c extension As above this file can be produced using data2config 51 97 RMCProfile Manual v6 4 6 4 2 RMC VERSION 6 FORMAT CONFIGURATION FILES 4 2 3 Version 6f format histogram file Normally users do not create the histogram files themselves but instead they are generated by
32. 0165 03942 23486 0 01 false false sf6190kbank2conv29p42rmc dat 88You may wonder what happened to versions 4 and 5 The answer is that as the code developed through versions A and 5 the input file format remained unchanged Said author recommends you jump there immediately 57 97 RMCProfile Manual v6 4 6 4 5 RMCPROFILE VERSION 3 FILES 1 3000 0 00165 03942 23486 0 01 false false sf6190kbank3conv29p42rmc dat 1 3000 0 00165 03942 23486 0 01 false false 0 no of coordination constraints 0 no of average coordination constraints true whether to use a polyhedra restraint 4 which restraint to use true whether to use bragg intensities gsas2 Which gsas profile function to use 10 10 10 Number of unit cell in each direction S Symbol for first atom use spaces to F Symbol for second atom use spaces to y whether to calculate from cfg at start 0 001 weighting factor false Convolute with profile function false Calculate the magnetic scattering 0 0 false Probability of swap moves auto tune percentage if greater than 0 0 I 2 Atom types to swap during swap moves The first line is a title then the number density of the configuration is given The next line contains the closest approach cut offs These are not necessarily the atomic radii since the crystal structure will define the nea
33. 1 1 1 63 GL 0 500000 0 500000 0 750000 7 1 1 1 64 one 0 750000 0 750000 0 750000 8 1 1 1 A number of points can be seen from this example The first line must contain the phrase Version 6f case sensitive All other keywords are case insensitive The metadata lines are not essential but given that the data2config program see section on utilities makes their use fairly easy you are recommended to use them Unless you keep very good notebooks and are equally good at keeping your file system in good order then it is folly not to avail yourself of the option to use metadata Remember the motto Don t cry later if you don t use metadata And if you wisely use the metadata lines the colons are essential The various lines beginning Number of are not necessary but will be automatically gener ated by RMCProfile in subsequent writes of the configuration file The Number density line is also not required but will be written by RMCProfile in sub sequent writes of the configuration file The Cell Ang deg line is essential if you don t include the Lattice vectors Ang data It defines the size and shape of the configuration in terms of the conventional crystallo graphic lattice parameters and will be used to create the lattice vectors If you include both the lattice parameters and lattice vectors the Lattice vectors Ang data will take precedence Both
34. 3 j The equation for G r can be expressed in a form with a constant offset 2 Gi 8 cicjbjbjgi r G r x on 4 4 IJ J which has limiting values Note that this differs from the definition by Keen by a normalisation factor we will discuss scaling by normalisation factors later 44 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES 2 G r 0 0 G r oo E98 4 5 4 1 7b Neutron scattering function The scattering function and the PDF G r are related by en E T 2 sin Qr i Q F Q p l 4nr2 r dr 4 6 and ot Ja Eau 4 7 2rp J lt Qr For dense materials the scattering function F Q has limiting values i Q gt 0 Loef i Q gt cl 4 8 The scattering factor can be written in a form with a constant offset to give 2 S Q i Q x ot 4 9 which has limiting values S Q gt 0 ong x cl S Q d cl 4 10 4 1 7c Alternative forms of the pair distribution function It is common to use two other definitions of the PDF functions ait sin QrdQ 4rrpG r 4 11 0 According to the definitions discussed by Keen the functions commonly written as i Q and F Q are synonymous The authors of this manuscript tend to use both functions Keen defines this in normalised form which we call Sporm Q in equation 4 19 below 45 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES and 2 T r Dir 4rrp x d 4rr
35. 38E 02 ttwhich clearly we are anticipating the user will have done 55 97 RMCProfile Manual v6 4 6 4 4 BRAGG SCATTERING 4 987625 4 33E 02 4 991615 4 27E 02 4 995605 4 23E 02 4 999600 4 26E 02 5 003600 4 30E 02 5 007606 4 35E 02 21 275999 2 34E 03 21 292999 1 12E 02 21 310051 2 57E 02 21 327099 2 65E 02 The first line contains four numbers The first gives the number of data points The second gives the number of the detector bank which is used to extract the correct instrument profile from the instr file described below The third parameter is the scale factor as calculated by GSAS and the fourth parameter is the volume of the unit Cell 4 4 20 back file As in Rietveld refinement the backgound is modelled using Chebychev polynomails This file contains the number of polynomials on the first line followed by the coefficients one per line 4 4 2c inst file This file is extracted from the GSAS files It has the form 4 1456 13 0 33 3 02 17 98 0 000000E 00 0 381440E 00 0 322500E 02 0 532200EE 02 0 000000E 00 0 204539E 03 0 000000E 00 0 000000E 00 0 126026E 02 0 000000E 00 0 000000E 00 0 000000E 00 DI GI The first line contains the number of detector banks in the instrument Then follows a block of five lines The first gives the bank number and the remaining four lines contain data that you as a user need not worry about This block is repeated for each data bank 4 4
36. 3Sr In this way the same constraint can be used to study Ca Sr _ TiO3 or any similar system To use this restraint option 2 needs to be specified in the dat file and poly tio and oti files supplied The poly file contains a title line which is ignored and the next line must contain the ideal Ti O bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the tetrahedral angle restraint e 300 The tio file contains a list of oxygen neighbours around each titanium atom and the ot i file contains a list of the titanium neighbours around each oxygen atom both of these files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 3 The CD restraint This restraint defines a configuration of unlinked tetrahedra formed from the first two atoms in the configuration As the name suggests it was first used for the study of deuterated methane To use this restraint option 3 needs to be specified in the dat file and poly cd and dc files supplied The poly file contains a title line which is ignored and the next line must contain the ideal CD bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the tetrahedral angle restraint Le 300 The cd file contains a list of deuterium neighbours around each carbon atom and the dc file contains a list of the carbon neighbours around each deuteriu
37. 4 3 1 Traditional RMC files These files have a very simple format The first line contains the number of points in the file and the second line is a title line These are followed by one line per data point each containing first the x values and the second the y values of the data For example a scattering data file might have the form 1975 KCN 250K with offset 0 01 0 52 0 4730834 0 54 0 4659694 0 56 0 4678035 0 58 0 4740225 0 60 0 474752 0 62 0 4666348 0 64 0 4686959 0 66 0 4683059 0 68 0 4674031 0 70 0 4667906 0 72 0 4660346 39 96 2 608086e 05 Chances are that the PDF file will begin with too many zero values for it to be an interesting example 53 97 RMCProfile Manual v6 4 6 4 4 BRAGG SCATTERING 39 98 0 002873718 40 00 0 004977553 etc 4 3 2 Data files generated by GUDRUN GUDRUN is the ISIS data correction and transformation toolkit for total scattering data The files generated by GUDRUN can now directly be read into RMCProfile rather than converted into the traditional format The subordinate keyword GUDRUN needs to be provided with the NEUTRONREALsPACEDATA and GEM12234 mdcs01 KCN in CCR at 20K I 12Wx34H chop 19302 0off 1939 1 2502 10 MGT QH DAK MTD ach 15 FEB 2003 02 14 23 spec bad groups_def dat 6 1 0 1700000E 02 0 0000000E 00 0 1456720E 01 0 0000000E 00 0 0000000E 00 0 5096614E 02 0 0000000E 00 0 0000000E
38. 6_300k xml Another usage might be S summon t dSpacing t diff_Bragg c rmcprofile config xml which will extract the arrays of d spacing and the difference Bragg profile i e difference between experiment and fitted function as comma separated arrays with each array enclosed within square brackets Use of o filename will cause the output to be written to a file which is probably more sensible for this particular case than listing to the screen In case it helps we give another similar example S summon t r t partial2 t partial3 c rmcprofile config 0 output txt xml This example extracts two partial PDF functions in order of distance followed by the two PDF func tions placing the output in the file called output txt It should be noted that arrays are written as comma separated values contained within square brackets Thus for example the command 74 97 RMCProfile Manual v6 4 6 5 2 TOOLS summon t numbers_of_species c rmcprofile config ag3cocn6_300k xml might return numbers_of_species 864 288 1728 1728 This might not be at least at first site very useful for Fortran or Excel users but it is in a form recog nised by many languages such as Python and can be transformed into something more useful Watch this space In some of the examples above we used a wildcard to specify the XML file ie x xm1 In so doing if this points to several XML files the result will be
39. CProfile when applied to crystalline materials is that it separately handles both the total scattering and the Bragg scattering Thus it make simultane ous use of the different information contained within these data concerning the distribution of the atomic positions in three dimensional space and their correlations For liquids and amorphous ma terials the information about the distribution of atomic positions is of no value and the structure is described entirely by the correlations between atomic positions Traditional crystallography is focussed only on the distribution of atomic positions The RMCProfile approach captures the best of both worlds particularly when applied to the study of disordered crystalline materials in which there are significant local fluctuations from the average structure In short RMCProfile can produce a configuration of atoms that is simultaneously consistent with both the long range and short range order of a material as reflected in the information contained in the data a truly holistic representation of the structure 1 2 4 RMCProfile ina nutshell In more detail RMCProfile offers the following features But we stress that it works perfectly well for liquids and amorphous materials 5 97 RMCProfile Manual v6 4 6 1 2 WHAT AND WHY OF RMC 1 Capacity to fit the Bragg profile directly as well as the total scattering 2 Capacity to fit both the scattering data and their derived pair distribution fun
40. EUTRON REAL _ SPACE DATA gt DATA_TYPE Gives the type of data options are G r T r Dir or G r together with the word normalised or normalized for functions that are scaled by the neu tron scattering coefficient X cjcjb b to give limiting values of 1 depending on the function This is ex plained in more detail in Section X gt CONSTANT_OFFSET If specified it allows the user to provide an offset that applies to the PDF data before fitting Default value is 0 0 if this keyword is not provided gt ENDPOINT End point of the data an integer gt FILENAME Filename containing the data gt FIT_TYPE Gives the function that is fitted options are G r T r D r or G r together with the word normalised Of normalized for functions that are scaled by the neutron scattering coefficient X c cjb bj to give limiting values of 1 depending on the func tion This is explained in more detail in Section X gt FITTED_OFFSET If specified this instructs the program to fit the offset value provided for this set of data Default is not to fit gt GUDRUN If specified the data file was generated by the Gudrun data reduction suite and contains errors on each point 36 97 RMCProfile Manual v6 4 6 gt NEUTRON_COEFFICIENTS gt NO_CONSTANT_OFF SET gt NO_FITTED_OFFSET gt START_POINT VM WEIGHT NEUTRON_RECIPROCAL_SPACE_DATA g
41. It is useful when it enables you to move lines be low this line rather than delete them should you possibly want to use them again can guess what this is supposed to do but don t know enough about this to be able to say what is needed Default is to not use this con straint if this keyword is not provided Introduces a block of subordinate keywords that switch on off various options Requires a number that indicates a version for the format of the input configuration file Al lowed values are rmc6f rmc3f and cfg The use of rmc c will be available soon the speed of which will be determined by the time it takes for someone to first ask for this There is no default version Requires text concerning the name of the per son running the simulation or experiment This is designed for your future benefit This is used for metadata and is not compulsory Requires text that act as keywords for your pos sible future benefit This is used for metadata and is not compulsory Introduces a block of subordinate keywords that define the parameters associated with a mag netic simulation Default is to not use magnetic spins if this keyword is not provided Requires text to act as a title for the material being studied This is used for metadata and is not compulsory Requires values of the maximum move of each atom Currently the units are not interpreted default units are Angstroms Requires numbers of the minimum approach
42. KCN_PDFpartials csv will contain the calculated partial pair distribution functions in CSV for mat KCN_PDF1 ecsv will contain the calculated and experimental data for the first file of PDF data in CSV format If more than one file of PDF data is used not a common case the number 1 will be replaced by the subsequent number of the data set KCN braggout will contain the calculated and experimental Bragg diffraction data KCN _bragg csv will contain the calculated and experimental Bragg diffraction data in CSV format KCN cssr which contains the configuration in a form that can be read by several visualisation programs including CrystalMaker which is endorsed by the authors hk1ls contains information used by the Bragg modules and which can be retained to be used by a subsequent run of RMCProfile KCN amp contains information used by the Bragg modules and which can be retained to be used by a subsequent run of RMCProfile These files will be described in subsequent chapters Comma Separated Values which is exactly as described by the name and is excellent because this format can easily be read into many analysis programs such as Microsoft Excel 9 97 RMCProfile Manual v6 4 6 CHAPTER 3 CAPABILITIES Chapter 3 Capabilities 3 1 Interatomic potentials 3 1 1 Why interatomic potentials In principle the RMC method should be sufficient to drive a simulation and in particular adding interatomic potentials to help drive
43. ON 6 ANALYSIS TOOLS HTML XHTML v5 standards will not give the desired rendering The XHTML file contains a readable report of the RMC simulation including graphs to report the progress of the simulation and plots of fitted data It contains a comprehensive set of the metadata input parameters step wise data and final parameters If the CML file is directed to include the configuration the report also contains an interactive three dimensional view of the configuration rendered using the Jmol tool but this may not be a good option for large files In short the resultant web report comprehensively extracts the essential information in a form that is easy to read Sample screen shots are shown in Figures 5 3 and 5 4 In the first shot the blue bars act as buttons to open up the report to show subsidiary data Graphs can then be displayed from the Show buttons In addition to providing an information centric view of the data obtained from the course of the RMC simulation ccViz provides a dictionary with definitions for all the terms By placing the mouse pointer over any term the relevant dictionary reference is displayed at the top of the right hand frame The idea is that RMC users should be able to share the reports with colleagues who are not expects our view is that output files should not need to be read hand in hand with the manual to make sense of them ccViz is supplied with the RMCProfile v6 package It does not need to be installe
44. Physics Condensed Matter 13 403 423 2001 5 M G Tucker M T Dove and D A Keen Application of the Reverse Monte Carlo method to crystalline materials Journal of Applied Crystallography 34 630 638 2001 6 M T Dove M G Tucker and D A Keen Neutron total scattering method simultaneous determination of long range and short range order in disordered materials European Journal of Mineralogy 14 331 348 2002 7 M G Tucker D A Keen M T Dove A L Goodwin and Q Hui RMCProfile Reverse Monte Carlo for polycrystalline materials Journal of Physics Condensed Matter 19 art no 335218 16 pp 2007 8 G Evrard and L Pusztai Reverse Monte Carlo modelling of the structure of disordered ma terials with RMC a new implementation of the algorithm in C Journal of Physics Con densed Matter 17 S1 S13 2005 9 M G Tucker M T Dove and D A Keen MCGRtof Monte Carlo G r with resolution correc tions for time of flight neutron diffractometers Journal of Applied Crystallography 34 780 782 2001 10 SA Wells M T Dove M G Tucker and K O Trachenko Real space rigid unit mode analysis of dynamic disorder in quartz cristobalite and amorphous silica Journal of Physics Condensed Matter 14 4645 4657 2002 96 97 RMCProfile Manual v6 4 6 11 An introduction to the use of neutron scattering methods in mineral sciences M T Dove European Journal of Mineralogy 14 203 224 2002 12 A
45. RMCProfile User Manual Code version 6 4 6 Matt Tucker Andrew Goodwin and Martin Dove January 15 2010 RMCProfile Manual v6 4 6 CONTENTS Contents 1 Introduction 2 1 1 Preface 2 1 2 What and why of RMC 2 2 Installing and Running RMCProfile 7 2 1 Installation 7 2 2 Running RMCProfile 7 3 Capabilities 10 3 1 Interatomic potentials 10 3 2 Magnetic structure modelling 18 3 3 Distance window constraints 26 4 Input Files 27 4 1 RMCProfile version 6 input files 27 4 2 RMC Version 6 format configuration files 48 4 3 Experimental data files 53 4 4 Bragg scattering 54 4 5 RMCProfile version 3 files 57 4 6 Upgrade to v6 61 4 7 Polyhedral restraints 62 5 Tools 68 5 1 Version 6 analysis tools 68 5 2 Tools 75 6 Examples 85 6 1 Overview 85 6 2 Example 1 SF 85 6 3 Example 2 SrTiO3 87 7 Appendices 88 7 1 Total scattering 88 7 2 Isotropic averaging 91 7 3 RMC method 92 7 4 Change log 93 8 References 96 1 97 RMCProfile Manual v6 4 6 CHAPTER 1 INTRODUCTION Chapter 1 Introduction 1 1 Preface This manual aims to tell you most of what you need to know about our implementation of the Reverse Monte Carlo RMC method in the RMCProfile program RMC is an approach that will require some investment on the part of the user at both the data collection and analysis stages Accordingly you will probably want to read most of this manual before you start This manual undertakes to describe the RMC method with some background
46. TEM gt MAGNETIC_ATOMS 4 1 RMCPROFILE VERSION 6 INPUT FILES Instructs the RMC simulation to attempt to adjust the initial configuration to best match the minimum dis tances Default setting is not to do this Instructs the simulation not to use the MOVEOUT op tion This is the default setting although not neces sary this keyword can be useful as a record for the user Instructs the to not program use the convolution of the experimental neutron reciprocal space data with the experimental resolution function This is the default setting although not necessary this keyword can be useful as a record for the user Instruct the program not to output a separate configu ration file at each save point during the run This is the default setting although not necessary this keyword can be useful as a record for the user Instruct the program to use the convolution of the ex perimental neutron reciprocal space data with the ex perimental resolution function The default is not to use the convolution Instruct the program to outputs a separate configu ration file at each save point during the run This is used in cases where it is necessary to collect multiple configuration files at equilibrium for analysis The different files are numbered e g aS rmc6f_01 rmc6f_02 etc The default is not to output these files Atom number followed by the seven coefficients for the expression for the magnetic form
47. a tabulation collation of values from each file This is extremely useful when merging data from many files A list of keywords for summon provided in rmcprofile config is given in Table 5 1 In fact this file can easily be edited to change the keywords or better still to add new keywords for existing quantities each quantity can be defined with an indefinite number of keywords It should be noted that for keywords with numbers if for a specific application there are not enough datasets defined in rmcprofile config it is an easy matter to edit the file to add new numbers 5 2 Tools Together with the main program a range of small programs are also supplied as tools to help with RMCProfile These tools fall into two main categories those to help setup the RMCProfile files before the program is run and those to help analyse the output from RMCProfile This section describes the programs supplied and how they can be used For Windows users the graphical programs supplied have been compiled using Cygwin a version of linux for windows This should not concern you apart from the files in the programs folder must all be kept together and an X server needs to be running before the graphics will be displayed An X server handles the graphics for unix in the same way that windows does on most PC There are many commercial versions available such as Exceed and Xwin32 however if you dont have one of these then we have supplied a basic version f
48. ain open as long as the X server is running this can be minimised as it will not be need again This is a very cut down version of an X server and we would recommend you use a full version such as eXceed Xwin32 or equivalent if you have them available 5 2 12 rmcplotm This a basic plotting program that can be used to plot information contained in the out and braggout file produced by RMCProfile provided at least one save cycle has been completed Once again it is actually a collect of programs that must all be stored in the same folder It requires an X server to be running and can be run in two ways The first way is on the command line by typing c rmcprofile tools rmcplotm rmcplotm bat lt lt stem name gt gt where stem name is replaced by the RMCProfile run name such as rmcsf6_190k in the above example again this assumes the program has be stored in c rmcprofile tools rmcplotm and if not then the correct path should be specified The second way to run the program is to right click on the out file select open with and then find and select the rmcplotm bat file A dos prompt window will then open and can be used to select the required plot In the plot interface left click allows you to zoom right click resets the view and middle mouse button exits from cursor 5 2 13 Atomeye This program has not been written by ourselves or any of the other RMC developers but is supplied with RMCP rofile because we
49. aks which arises from the static or mean atomic scattering and inelastic scattering which arises from dynamic processes The Fourier transform of the total scattering measurement provides information about the relative positions of atoms which can usually only be interpreted over short distances Billinge and Thorpe 1998 Dove 2002 Until recently total scattering experiments were mostly associated with studies of fluids or glasses Chieux 1978 Wright 1993 1994 1997 In contrast diffraction studies of crystalline materials tend to be primarily focused on the measurements of the Bragg peaks with little concern for the shape of the background provided that it could be fitted by an appropriate polynomial The Bragg peaks give information about the distributions of positions of atoms within the unit cell and for many purposes this is exactly all the information that is required Since fluids and glasses do not have long range periodic order there are no Bragg peaks One of the exciting developments in crystallography over recent years has been the application of total scattering methods to crystalline materials Billinge and Thorpe 1998 particularly for crystalline materials that have a high degree of structural disorder The subsequent coupling of total scattering measurements to modelling through the RMC method has extended the opportunities for studying disordered crystalline materials at an atomistic level The information contained wi
50. ant As in the bonds file the Metadata lines are important to link this file with the actual simulation but will be ignored by RMCProfile The two lines containing the number of atoms and number of triplets are important and must be accurate The line of dots is used to divide the header from the data So now we consider the actual triplets data For each triplet type there is a list of all the atoms in the same order as the configuration if you break this order that will be recognised and the program will abort Unlike the bonds file we have two lines for each atom This is because an atom can be either at the centre of a triplet or at the end The first line describes the atomic connectivity when the atom is at the centre of a triplet and the second line describes the atomic connectivity when the atom is at the end of a triplet Consider the following pair of lines for one atom Zan 1 4 101 C T02 Cp 101 CG 103 C 7 101 104 C 101 C 105 C 4 An 1 ss 0 The first line describes the connectivity when the atom Zn in this case is at the centre of a C Zn C triplet The first number specifies the atom number in the configuration file and this is followed by the chemical element symbol Zn in this case The third number gives the number of the triplet type as determined by the order in which the gt ANGLE line occurs in the data file In this example we are looking at the first atom in the configuration which h
51. appens to be a zinc atom and this pair of lines is concerned with the first triplet specified in the input file The double colons are important because they separate the description of the data to the left from the actual bond data on the right Consider the last number This gives the number of triplets which involve the atom In this example the Zn atom occurs as the centre of 4 triplets from the first 15 97 RMCProfile Manual v6 4 6 3 1 INTERATOMIC POTENTIALS line and is never at the end of the triplet as specified by the zero in the second line The triplets are all of the form C Zn C Now consider a second example 101 G sa 1 Zn 20L C 101 C 13 201 C 2 Zn These lines describe the second triplet defined in the data file namely C C Zn linkages and are concerned with carbon atom that is atom number 101 in the configuration The first line describes the way that this atom is at the centre of a triple and bonded to Zn atom 1 and C atom 201 This atom is the centre of only one triplet The second line describes the way that this atom is at the end of the triplet bonded to C atom 201as the centre of the triplet and Zn atom 2 at the other end Ideally you should not need to edit this file but if something in your system is more complicated then sadly you will have to do some hand work 3 1 6 Visualisation of bond orientation distribution functions RMCProfile allows for easy plotting of bond orientatio
52. arting configuration of atoms for RMCProfile building a supercell of a specific crystal structure and writing out a clas sic version 3 cfg file As you will see below crystal has many disadvantages compared to data2config it requires more effort from the user it only generates version 3 files and it gives you nothing else but hey it costs us nothing to give it away And if you like nostalgia this is for you The structure must be defined in P1 symmetry with the lattice parameter defined in a vector format An example input file for the BCC structure of SFe is shown below 10 10 10 5 88677 0 00000 0 00000 0 00000 5 88767 0 00000 0 00000 0 00000 5 88767 2 2 0 00000 0 00000 0 00000 0 50000 0 50000 0 50000 12 0 25102 0 00000 0 00000 0 25102 0 00000 0 00000 0 00000 0 25102 0 00000 0 00000 0 25102 0 00000 0 00000 0 00000 0 25102 0 00000 0 00000 0 25102 0 75102 0 50000 0 50000 0 24898 0 50000 0 50000 0 50000 0 75102 0 50000 0 50000 0 24898 0 50000 0 50000 0 50000 0 75102 0 50000 0 50000 0 24898 0 sf6_190k cfg 81 97 RMCProfile Manual v6 4 6 5 2 TOOLS The first line contains the number of unit cells required in each direction Since this example is cubic the number in each direction is the same however for more complex systems the numbers should be chosen to produce a configuration box with approximately equal sides This is due to the fact the RMCProfile calculates the partial
53. ary ex perimental data being total scattering data McGreevy amp Pusztai 1988 McGreevy 1995 Mellergard amp McGreevy 1999 2000 McGreevy 2001 The starting point is some configuration of atoms that has the correct density and in the case of a crystalline system a confining box that has the dimen sions that are some integral multiple of the experimental lattice parameters During an RMC simulation the atomic coordinates are varied in a random manner in order to improve the best agreement with experimental data We write any experimental quantity as VE and the corresponding calculated quantity as y We then define an agreement factor as is De ve o 7 20 j where we sum over all data points labelled by j and gj is a weighting factor which may correspond to the experimental uncertainty on y Clearly the best final configuration is that for which the value of x is a minimum as in any data fitting technique In the Monte Carlo approach the calculated values of y are changed through the random changes in the configuration If the change lowers the value of x the change to the configuration is accepted On the other hand if the change to the configuration causes x to increase by an amount Ax the change is not automatically rejected but accepted with the probability P exp Ax 2 7 21 This ensures that the model does not get trapped in a local minimum and enables the model to converge towards the global minim
54. ask for the following information 1 The name of the histogram file it http www lemkesoft com 17 97 RMCProfile Manual v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING 2 The name of the required output file which much have extension ppm for the graphics con version programs to work 3 The required number of pixels along an edge of the plot which always has square shape 4 Values of angle 0 and o throughwhich to rotate the sphere 5 Option to change the maximum and minimum values of the bond odf that correspond to the extreme colours being used 6 Background colour 7 Option to rotate the plot in order to produce an animated gif file This generates the PPM file which you can then convert to a graphics file in a standard format using the methods described in the previous section 3 2 Magnetic structure modelling 3 2 1 Introduction The use of RMCProfile to refine magnetic structures is based on the notion of pairing each atom istic configuration with a corresponding supercell spin configuration The positions of the magnetic moments in the spin configuration are then determined by the positions in the atomistic configu ration Each RMC move involves either a change in atomic positions or magnetic moment orien tations The relative frequency of each choice is left as a user defineable parameter Naturally displacement moves of non magnetic species do not affect the magnetic scattering functions nor do spin
55. ation tool subsection 5 2 3 The output files all have the same seed name For example the command data2config diag cssr rmc4f nacl cif will produce the configuration files nacl cssrandnacl rmc4f andthe diagnostics file nac1 out Simply typing the command dat a2config will produce a list of allowed options and input file types which means that you don t need to have the manual at hand when running the program 5 2 1b Usage When you run data2config you will be asked a small number of questions These include e The size of the supercell defined by three indices that specify the expansion of the unit cell along each of the three lattice vectors e Various metadata items such as the owner of the data useful when you want to come back to a configuration file later the name of the material a title a comment etc Some of these metadata items are collected from the input file or else cannot be included in any of the configuration files and thus the specific metadata queries asked will depend on the context You are allowed to give blank replies in which case the metadata will be ignored Such a course of action would be naughty and should make you feel ashamed Remember saving 10 seconds now may cause you hours of grief in a few months time 78 97 RMCProfile Manual v6 4 6 5 2 TOOLS e If your input file is a classic version 3 configuration file you will be asked for the names of the atoms e If data2config
56. bours This constraint is consistent with the position and integral of the first two peaks in the PDF for silica corresponding to the Si O and O O nearest neighbour distances with four oxygen atoms arranged in a tetrahedral arrangement about the central silicon atom The third peak corresponds to the shortest Si Si distance and analysis of this peak tells you that neighbouring SiO tetrahedra are linked at corners with an Si O Si angle of around 145 Although this is nice information it doesn t tell you much that you couldn t have previously guessed given that this is exactly as found in crystal structures What RMC will give you is information on how pairs of tetrahedra are linked together in a three dimensional structure to form a larger connected network and there is no other technique that can provide this information The RMC method gives a snapshot view of 104 atoms and if the fit is consistent with all the data available then the configuration will have the characteristics of the sample being studied Of course this number of atoms is a lot smaller than you would find in an experimental sample and throughout the RMC simulation the positions of the atoms will fluctuate in a way that resembles thermal motions across the larger sample Thus if an RMC simulation is run again from scratch or for a different length of time at equilibrium a slightly different snapshot will be produced where the atoms will have moved to different positions alb
57. cannot successfully extract the element extracted from the atom labels given in the input file you will be asked for the name of the atom Input files will typically contain atom labels such as C2 to represent the second carbon atom in the file from which data2config will attempt to extract the chemical symbol for the element If labels do not contain the element symbol in an unambiguous way data2config will either extract an element symbol regardless or else will ask you to provide the element symbol This labels of the form C2 or C1N2 will produce the element carbon but a label of the form 12c will ask for the element To assist cases where there is ordering of vacant sites the symbols Va or VA will be interpreted as vacant sites We would remark that not only can data2config be used to produce configuration files from the raw crystal structure data files in order to initiate a new RMC run but it can also be used to convert legacy classic version 3 configuration files into the newer version 4 configuration files 5 2 1 Simple file format files The SFF format is designed to allow you to construct an input file with minimum of effort Unlike the input file for the crystal program you do not have to do much work to produce an SFF file The format of the SFF file is most easily described with reference to an example cell 5 68 5 68 5 68 90 0 90 0 90 0 symmetry 4 X Vr Z 1 24x 1 2 y Z 1 2 x y 1 2 z x 1 2 y 1 2 z atom
58. ch reflect a different approach to managing configuration files These are somewhat richer than the classic Version 3 format files described later 4 2 1 Version 6f format configuration file This format is best described with reference to an example file Version 6f format configuration file etadata tile NaCl in a small box etadata owner Martin Dove etadata date 15 02 2009 etadata material NaCl etadata comment This is a test configuration etadata source Solid State Physics text book Number of moves generated 0 Number of moves tried 0 48 97 RMCProfile Manual v6 4 6 4 2 RMC VERSION 6 FORMAT CONFIGURATION FILES Number of moves accepted 0 Number of prior configuration saves 0 Number of atoms 64 Supercell dimensions 2 2 2 Number density Ang 3 0 043656 Cell Ang deg 11 360000 11 360000 11 360000 90 000000 90 000000 90 000000 Lattice vectors Ang 11 360000 0 000000 0 000000 0 000000 11 360000 0 000000 0 000000 0 000000 11 360000 Atoms 1 Na 1 0 000000 0 000000 0 000000 1 0 0 0 2 Na 1 0 250000 0 250000 0 000000 2 0 0 0 3 Na 1 0 250000 0 000000 0 250000 3 0 0 0 4 Na 1 0 000000 0 250000 0 250000 4 0 0 0 5 Na 1 0 000000 0 000000 0 500000 1 0 0 1 6 Na 1 0 250000 0 250000 0 500000 2 0 0 I 58 Cl 0 500000 0 750000 0 000000 6 1 1 0 59 Cl 0 500000 0 500000 0 250000 7 1 1 0 60 Cl 0 750000 0 750000 0 250000 8 1 1 0 61 el 0 750000 0 500000 0 500000 5 1 1 1 62 EL 0 500000 0 750000 0 500000 6
59. containing the Bragg diffraction data section 4 4 KCN inst containing information on the instrument resolution function in the format as provided by the GSAS Rietveld refinement code subsubsection 4 4 2c KCN hk1 containing information on the range of Bragg peaks to be considered in the analysis of the Bragg diffraction data this shortly to be incorporated into the main dat file subsubsec tion 4 4 1a KCN dw containing information on the distance window constraint as described in section 3 3 this will shortly be incorporated into the main dat file The KCN stem part of the file names can be anything you like but as in this example this group of files must have the same stem name These files are described in the chapters and sections indicated above 2 2 2 Running RMCProfile To run RMCProfile execute the following shell command rmcprofile KCN gt KCN log The part of the line gt KCN 1og tells the command to direct the standard output to a specified file here called KCN log but which actually could be called anything you like If this part of the line is not included the standard output goes directly to your screen In this example we have assumed that the program file here called rmcprofile but which could be called anything you want to rename it to will be automatically picked up by the command interpreter which means that it will either be in a special directory that is included in your PATH or is in your
60. ctions 3 Able to take account of instrument resolution 4 New to version 6 4 the incorporation of generalised molecular constraints for bond lengths and angles 5 Also new to version 6 4 the ability to correct the experimental data for the effects of finite configuration size 6 Incorporation of model specific data based polyhedral constraints eg when studying materi als containing molecular species such as NaNOs or framework materials containing struc tural polyhedra such as phases of silica 7 Ability to model spin configurations for magnetic materials 8 Ability to study systems with site disorder such as cation disorder or vacancy inclusion 9 Ability to use a wide range of experimental data including both x ray and neutron diffraction and XAFS data 10 Ability to use bond valence sums 11 XML output for data visualisation and analysis This manual is primarily focussed on Version 6 4 of RMCProfile which represents a significant departure from the previous version Version 5 here called the classic version The classic version of RMCProfile retained the same form of input file as was used in RMCA and the code base was essentially that of RMCA with additional subroutines for new functionality Although Version 6 4 is not a complete rewrite of the code it was nevertheless a major revision including conversion to Fortran95 which as previously mentioned required a lot of reorganisation and rewritin
61. cy disorder At its heart the RMC method is easy to understand Essentially a configuration of atoms is modi fied by successive steps until properties calculated from it are in best agreement with experimental data In the most common application the property is either the pair distribution function or its Fourier transform as measured in a neutron or x ray total scattering experiment These data pro vide information about the short range atomic structure of matter bond lengths numbers of atomic neighbours layering of shells of neighbours about a central atoms etc and fluctuations in this structure Some of this information can be derived directly from calculations based on the pair dis tribution function for example the first 1 3 peaks will give you information about the molecular fragments that any disordered matter is built from but this information doesn t lead directly to a model Crystallographers have an advantage here because they can go from their diffraction data directly and nowadays often quite quickly to a model of the atomic structure that extends through out space RMC was designed to fill this void for liquids and amorphous materials but it became clear that the method could provide unique information about disordered crystalline materials too The name of the RMC method gives away the fact that the process of building the atomic model relies on a Monte Carlo algorithm This is an iterative approach in which success
62. d instead it should simply be placed in a location from which it can be treated as a shell command ccViz can also be downloaded from http uszla me uk space software ccViz and compiled from source To conclude this section we note that ccViz can be used with a variety of different atomic scale simulation outputs examples include CASTEP SIESTA and DL_POLY3 5 1 3 The summon tool summon is another python program that can be used to extract desired data from a CML file without having to browse through it with a text editor or do the same through one of the standard output text files It can be compared with grep for text files One key application of this is to extract information from a group of files when many jobs have been run as part of a single study It replaces the standard approaches of writing bespoke applications of scripts to parse a file and extract the desired information or the even more depressing approach of cutting and pasting between the text view of the output file and the spreadsheet Not only will summon save a lot of effort it will also prevent mistakes that can occur when using bespoke programming or cut and paste approaches The summon package needs to be installed on your computer It wraps up a number of required packages and installs summon as a shell command using the make install command To explain how summon works we should start with an example of using summon as a shell com mand with simple para
63. d to look at this another tweak doubt that restarting from his6f works because need to copy some fixes from the rmc 6f code would like to see that the rmc6 stuff works first another tweak would like to put the experimental data into the csv format realise writing this that haven t thought about when you have several data files another tweak also don t have some of this output stuff working with x rays so need to chat about this another tweak now write out the PDF functions with the same value of r as used in the code want to check again on how it handles Q I did check this once but will do this again as a tweak 95 97 RMCProfile Manual v6 4 6 CHAPTER 8 REFERENCES Chapter 8 References 1 R L McGreevy Reverse Monte Carlo modelling Journal of Physics Condensed Matter 13 R877 R913 2001 2 D A Keen M G Tucker and M T Dove Reverse Monte Carlo modelling of crystalline disor der Journal of Physics Condensed Matter 17 S15 S22 2005 3 M G Tucker M T Dove and D A Keen Simultaneous analyses of changes in long range and short range structural order at the displacive phase transition in quartz Journal of Physics Condensed Matter 12 L723 L730 2000 4 M G Tucker M D Squires M T Dove and D A Keen Dynamic structural disorder in cristo balite Neutron total scattering measurement and Reverse Monte Carlo modelling Journal of
64. data Indicates that XML output in the language of the Chemical Markup Language CML is required the default in the absence of this keyword is not to create a CML file CML is described in a later section This keyword can be followed by a block of subordinate keywords Although op tional we recommend the use of this keyword because XML opens up a whole new world of possibilities for data analysis CML is discussed in section 5 1 1 Requires text that acts as any comment you want to make An example might be that the specific run is part of a larger study This is used for metadata and is not compulsory Requires a number that indicates a version for the data format Allowed values are rmc 6f rmc3f and cfg The use of rmc c will be available soon the speed of which will be deter mined by the time it takes for someone to first ask for this There is no default version Requires text that allows the user to attach a one line note about the data For example you could note that the data quality is good or of lower quality just for testing purposes This is used for metadata and is not compulsory 29 97 RMCProfile Manual v6 4 6 END FIXED_COORDINATION_CONSTRAINTS FLAGS INPUT_CONF IGURATION_FORMAT INVESTIGATOR x EYWORDS MAGNETISM MATERIAL MAX IMUM_MOVES MINIMUM_DISTANCES 4 1 RMCPROFILE VERSION 6 INPUT FILES Indicates that this is the last line to be read
65. distance of 1 61 A The difference between the distance between mean positions and the mean distance between instantaneous positions reflects the existence of considerable disorder on a short length scale that arises from large amplitude fluctuations of the structure What tools do we have to study this disorder in a way that leads to atomic models You guessed RMC and only RMC 1 2 3 How RMCProfile fits into the picture The original code for RMC was RMCA and was designed for the study an amorphous and fluid matter We started to develop RMCProfile as a significant extension of the original RMCA code in order to add support for new functionality particularly to model crystals 5 7 In principle we could simply have used RMCA for this but we wanted to exploit the information that is specifically contained in the Bragg peaks separately from its contribution to the total scattering Since then we have added a lot of new functionality and we have also converted the code from Fortran77 to Fortran95 which has led to significant changes deep in the heart of the program RMCA is no longer being developed and is not supported Thus RMCProfile 7 should be seen as the evolutionary successor to RMCA and used in preference to RMCA an alternative code developed by one of the core developers of RMCA is RMC 8 and if you are not interested in crystalline you might like to take a look at this code As we have just said the key feature of RM
66. duction suite and contains errors on each point Requires list of neutron scattering coefficients prod ucts of scattering lengths and number concentrations for all atom pairs particular to this data set only The data are allowed to straddle several lines of the file Default units are 10 20 m The default values are cal culated by the code if this keyword is not given see section 4 1 6 Instructs the code that no offset is to be applied to the scattering data before fitting This is the default setting although not necessary this keyword can be useful as a record for the user Instructs the program not to fit any offset value on the scattering data This is the default setting although not necessary this keyword can be useful as a record for the user Instructs the program not to fit a scale factor for the data This is the default setting although not neces sary this keyword can be useful as a record for the user Start point of the data provided as an integer Parameter that weights the data in the simulation 38 97 RMCProfile Manual v6 4 6 gt ANGLE gt ANGLE_SEARCH gt PLOT gt STRETCH gt STRETCH_SEARCH gt TEMPERATURE SWAP The US spelling color will also work 4 1 RMCPROFILE VERSION 6 INPUT FILES This gives the parameters in the bond angle poten tial energy function You give in this order the ele ment symbol of the central atom lab
67. e followed by a block of subordinate keywords Do not provide if you have no X ray reciprocal space data Note that the order of the atoms must be the same as the order of atoms in the configuration file Note that the order of the atom pairs is set by the order of atoms in the configuration file This is illustrated by the example of 4 atoms labelled 1 2 3 4 with the order of pairs being 1 1 1 2 1 3 1 4 2 2 2 3 2 4 3 3 3 4 4 4 4 1 4 Subordinate keywords Like the previous section this is also boring but essential and comprehensive Each block of sub ordinate keywords is given under the corresponding major keyword Note that not all keywords require the characters these are only used if they are to be followed by data on the line Also note that some keywords particularly those beginning with the characters No merely replicate the default behaviour but can be useful as a record of the user s explicit intentions BRAGG gt BRAGG_SHAPE Give a text string to denote the type of profile line shape to use Options are GSAS1 GSAS2 XRAY1 and XRAY2 as defined by the GSAS manual The case doesn t matter gt DMIN Give the minimum d spacing value to be used in the analysis of the Bragg diffraction data Users can use the QMAX subordinate keyword instead The use of this subordinate keyword will replace the need for the hk1 file gt HKL_RANGE Give in order the maximum values of the Mi
68. e if your data has the points defined at the bin edge and RMCProfile requires it to be defined at the bin centre then you could add or subtract half a bin width whichever is appropriate It is run at the command line and requests the information needed 5 2 6 get gsas bragg This program is used to extract the information required by RMCProfile from a GSAS refinement to enable the Bragg profile to be fitted It requires that GSAS is installed on the same machine you are running it on Again it is run on the command line in the same directory as the GSAS refinement files and requires at least the EXP and required data file to be present It will then run GSAS through once cycle of powpref and genles if this has not already been done To run the program simply type get_gsas_bragg on the command line and hit return assuming the program is in the current path or directory it will then ask for the required information and produce the bragg back hk1 and inst files If the GSAS executable are not in c gsas exe then their location needs to be entered after the program name before hitting return Le get_gsas_bragg d my_gsas_exe 5 2 7 lattice_vectors This program outputs the lattice vectors required for the crystal program if supplied the lattice pa rameters from a GSAS refinement or elsewhere As with the other programs it is run on the com mand line and asks for the required information 5 2 8 neighbour_list This program shou
69. e atom All of these neighbour files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 67 97 RMCProfile Manual v6 4 6 CHAPTER 5 TOOLS Chapter 5 Tools 5 1 Version 6 analysis tools 5 1 1 CML files RMCP rofile produces a number of standard output files in text form With the use of the CML keyword RMCProfile will also generate a file containing a rich set of output data in the Chemical Markup Language CML format CML is an XML language designed to represent chemical data and adapted for atomistic simulation CML files are not designed to be read by humans but are readable because each item of data is enclosed within descriptive tags Sample extracts of an RMCProfile CML file are shown in Figures 5 1 and 5 2 You can see that each item of date is properly described within the CML file For example in Figure5 1 you can see that there is a block of metadata items contained within the lt metadataList gt tags with general format lt metadataList gt lt metadata name content gt lt metadataList gt Examples in Figure 5 1 include the metadata items that are provided in the input file such as the item given in the MATERIAL keyword line plus other metadata items generated by the code itself such as the code name and version items In Figure 5 1 you can also see a set of input parameters that are nested within the lt parameterList g
70. e output file mno out which includes the fit to data shown in Fig 3 4 There is rea sonable agreement over most values of Q except between 0 lt Q lt 3A where the key magnetic structure reflection is not modelled well at all S Q o 5 10 15 20 25 Q A 1 Figure 3 4 Initial RMC fit to neutron scattering data for MnO Data are shown as solid points the RMC fit as a red line and the difference data fit shown as a green line shifted by 2 units RMC refinement In order to proceed with a refinement of the magnetic structure we must edit the mno dat file to tell RMCProfile how long to run the refinement and also how often to save The relevant line in the parameter file is 0 0 Time limit step for saving which we change to DL Time limit step for saving It so happens that five minutes is sufficient in this simple case to arrive at a reasonable fit to the magnetic structure More complicated structures will take longer We run the program as before using the command rmcprofile mno The fit should have converged within five minutes with a goodness of fit reducing from its initial value x 395 9 to x 12 If the value of x is significantly larger than this value it might be worth running RMCProfile once more 22 97 RMCProfile Manual v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING Analysis First we can take a look at the new fit to data once again by plotting the values given in mno datja representat
71. e user gt START_POINT Start point of the data provided as an integer v WEIGHT Parameter that weights the data in the simulation Note that the order of the atom pairs is set by the order of atoms in the configuration file This is illustrated by the example of 4 atoms labelled 1 2 3 4 with the order of pairs being 1 1 1 2 1 3 1 4 2 2 2 3 2 4 3 3 3 4 4 4 Additional units can be made available on request but internally the program works in terms of kJ mol Note that the order of atoms is set by the configuration file 4 1 5 Example files This is an example of a simulation of Agg3Co CN g RMC refinement of Ag3Co CN 6 format A d i d i dp Using new input TITLE Ag3CoCN6_300K MATERIAL AG3 CO CN 6 PHASE TRIGONAL TEMPERATURE 300 K PRESSURE AMBIENT DATA_NOTE Data collected August 2007 RMC_NOTE First attempt to fit data KEYWORDS Ag3Co CN 6 First attempt COMMENT Refinement without peak broadening INVESTIGATOR Andrew Goodwin and Matt Tucker NUMBER_DENSITY 0 052612 Angstrom 3 MAXIMUM_MOVES 0 0149 0 0200 0 0445 0 0411 Angstrom R_SPACING 0 020 Angstrom PRINTING_PERIOD 10000 TIME_LIMIT 0 0 MINUTES SAVE_PERIOD 0 0 MINUTES ATOMS Ag Co C N NEUTRON_REAL_SPACE_DATA 1 41 97 RMCProfile Manual v6 4 6 4 1 RMCPROF ILI E VERSION
72. e weighting for the octahedral angle restraint e 300 The following line must contain the ideal P O bond distance to be used the weighting for this bond restraint and then the weighting for the tetrahedral angle restraint The zro file contains a list of oxygen neighbours around each zirconium atom and the ozr file contains a list of the zirconium neighbours around each oxygen atom Similarly the po file contains a list of oxygen neighbours around each phosphorous atom and the op file contains a list of the phosphorous neighbours around each oxygen atom All of these neighbour files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 8 The ZrW2Os restraint This restraint defines a network of linked octahedra and tetrahedra formed from the first three atoms in the configuration as the name suggests it was first used for phases of ZrW20g This restraint differs from the ZrP207 version since one of the tetrahedral oxygens is non bridging To use this restraint option 8 needs to be specified in the dat file and poly zro ozr wo and ow files supplied The poly file contains a title line which is ignored and the next line must contain the ideal Zr O bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the octahedral angle restraint e 300 The following line must contain the ideal W O bond distance to be used the we
73. ecific stored version No parameter is re quired if the ccviz command is already installed in a location picked up in your search path For this to work it is required that mkt emp is installed on the computing running the code Default is not to perform this action gt INPUT_CONFIGURATION Instructs the code to read the configuration from a CML file Default is to read from a standard config uration file not yet implemented gt REPORT_CONFIGURATION Instructs the code to save the configuration in the main CML file for subsequent visualisation using the ccViz tool described later This is not recommended except for the use of small configurations Default is not to save the configuration in the main xml file not yet implemented gt OUTPUT_CONF IGURATION Instructs the code to write the configuration into a CML file Default is to write to a standard configu ration file not yet implemented FLAGS gt CSSR Instructs the program to write a copy of the final atomic configuration in cssr format suitable for view ing in a molecular plotting program such as Crystal Maker Default is not to produce this file 34 97 RMCProfile Manual v6 4 6 gt MOVEOUT gt NO_MOVEOUT gt NO_RESOLUTION_CONVOLUTION gt NO_SAVE_CONF IGURATIONS gt RESOLUTION_CONVOLUTION gt SAVE_CONFIGURATIONS MAGNETISM gt FORM_FACTOR gt FORM_FACTOR_F ILE gt MAGNETISM_FILE_S
74. ed the actual magnitude of a spin comes from the values given in the MAGNETIC_ATOMS keyword in the input file 2 The magnetic form factors can be calculated by RMCProfile using the standard analytical formula f Q Aexp aQ 167 Bexp bQ 167 C exp cQ 167 D 3 10 where A a B b C c D are empirical coefficients as defined in e g Acta Cryst A27 545 1971 Alternatively it is possible for the user to provide their own form factors as a separate file so long as these are given for precisely the same Q values as in the neutron scattering data The relevant flags are discussed in section 4 1 above E The order of the magnetic atoms in the RMC configurations is important in that all the mag netic atoms must be given first Naturally the order of the atom types in the spin configuration files must be the same as the order of the magnetic atom types in the nuclear RMC configu rations 19 97 RMCProfile Manual v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING 4 In general magnetic structure refinement takes a substantially longer time than nuclear refine ment and there is a significant degree of interplay between the nuclear and magnetic struc tures A reasonable general approach appears to attempt refinement of the nuclear structure first using random spin orientations but not refining these Once the nuclear refinement appears to have reached equilibrium one might then consider either refining the spin
75. ed by the crystal tool for generation of ver sion 3 configuration files described later The output filename has the extension cfgcom To be fair there was a time when crystal was all you could have but there were times when the only means of transport besides foot was horseback 77 97 RMCProfile Manual v6 4 6 5 2 TOOLS sort diag noannotate sort the atoms by atom type before being written to the configuration file this is selected by default when the rmc3 option has been selected write a diagnostics file it isn t worth reading because there is a lot of du plicate data but is useful if you have problems request no annotations to be added to the configuration files It is set as a long flag because in the view of the code s author you have to be somewhat reckless not to properly annotate your file with useful metadata Any number of options can be selected for example Allowed input file types are denoted by the name extensions and these are H BL Or tbl CIF Or cif SFF or sff CFG Or cfg CFGCOM or cfgcom files produced by GSAS we anticipate that many users of RMCProfile will have run a prior Rietveld refinement CIF crystal information file format the format favoured by many databases such as the Inorganic Crystal Structure Database our own simple file format Subsubsection 5 2 1c RMC v3 configuration file Input file for the crystal configuration gener
76. ed in the dat file and poly alo oal po and op files supplied The poly file contains a title line which is ignored and the next line must contain the ideal AlI O bond distance to be used the weighting for this bond re straint Le 100 and then the weighting for the tetrahedral angle restraint e 300 The following line must contain the ideal P O bond distance to be used the weighting for this bond restraint and then the weighting for the tetrahedral angle restraint The alo file contains a list of oxygen neigh bours around each aluminium atom and the oa1 file contains a list of the aluminium neighbours around each oxygen atom Similarly the po file contains a list of oxygen neighbours around each phosphorous atom and the op file contains a list of the phosphorous neighbours around each oxy gen atom All of these neighbour files should be generated using the neighbour _list program supplied with RMCProfile and described in section 5 2 4 7 6 The PZT restraint This restraint defines a network of linked octahedra formed from the second third and fourth atoms in the configuration as the name suggests it was first used for phases of lead zirconium titanate PbZr Ti _ O3 This differs from the SrTiO3 restraint in that the network consists of octahedra of two sizes one for the ZrOg and one for TiOg To use this restraint option 6 needs to be specified in the dat file and poly zro ozr tio and oti files supplied The
77. eit within the constraints of the data being fitted By collecting many independent configurations it becomes possible to do some powerful analysis in the same way that many configurations are analysed in any simulation based on thermodynamics For example recently RMC has been used to extract dynamical information from a collection of static configuration snapshots The authors of this manual have a strong interest in disordered crystals 2 You might think that crystals are already catered for by standard crystallography tools based on x ray and neutron 4 97 RMCProfile Manual v6 4 6 1 2 WHAT AND WHY OF RMC diffraction but things are not this simple Traditional Bragg scattering provides information about the distribution of atomic positions In most cases this means that diffraction will tell you about the av erage positions of atoms and their mean square displacements due to thermal motions However Bragg diffraction contains no information about the correlated motions of atoms This is illustrated with a vengeance in the case of high temperature crystal polymorphs of silica such as beta quartz 3 and beta cristobalite 4 If you take the crystal structure and calculate the distance between the average positions of the closest silicon and oxygen atoms you get a value of around 1 55 A Often this distance is associated with the bond length However the PDF which is a true mea sure of the average instantaneous bond length gives an Si O
78. el followed by the element symbols of the two bonded atoms followed by the value of the force constant K in units of ev or kJ mol which need to be stated the equilibrium bond angle On in units of deg followed by the two bond lengths in units of Ang which must be stated Give the range of values of angles around the equilib rium angle Oo that will be searched in the initial bond search task The value can be in a percentage in which case give the units as or deg This provides information for producing stereographic plots of bond orientation distribution functions Give the following information using the words pixels lt value gt with the default value being 400 colour lt value gt where allowed colours are charcoal default red green maroon and pink zangle lt value gt and zrotation lt value gt to give the angle that the plot is rotated away from and about the z axis with the choice of units being deg or rad This gives the parameters in the bond stretch poten tial energy function You give in this order the atom labels followed by the value of the energy of the bond D in units of eV or kJ mol which need to be stated and finally the equilibrium bond length ro in units of Ang which must be stated 7 Give the range of values of distances around the equi librium distance ro that will be searched in the initial bond search task The value can be in a percentage in which case give the
79. elow b where the are followed by some data for example MATERIAL Quartz The parser will know what to expect whether characters or numbers c where the major keyword is followed by a block of multi line data In this case the subordinate keywords are designated by the preceding gt character described next gt This denotes a subordinate keyword and is tied to a major keyword The order of the subor dinate keywords is completely arbitrary within the block but they have to follow immediately after the associated major keyword In the examples shown on page 27 the FLAGS key word line is followed by a set of lines for which each subordinate keyword is merely a directive in this case the subordinate keyword doesn t need the symbol hopefully this isn t too inconsistent for people but at least an inconsistency is offset by the fact that there are very few rules On the other hand the NEUTRON_REAL_SPACE_DATA 1 major keyword is followed by a set of subordinate keywords which in turn have associated data following the rule for the use of as above Thus the line gt WEIGHT 0 02 is the way to input a value for the weighting parameter associated with this neutron data set The only other rule is the use of the END line This tells the input parser to ignore anything below this line which is useful when playing around Subject to these two rules there are many
80. ent and f Q the magnetic Q dependent scattering form factor The real space functions A r and B r essentially measure the magnitude of spin spin correlations perpendicular to and parallel to the vector that joins each pair of magnetic atoms They can be calculated directly from the RMC configurations and function as magnetic analogues of the nuclear pair distribution functions The magnetic contribution to the Bragg intensities is calculated using what is also a standard ap proach The key equation involved is 2 1 Q 5 Y ayPj Q exp iQ vii 3 7 j where the magnetic interaction vector qj is given by mj Q Q m qj 7 Q2m 3 8 and mu is the spin vector of the magnetic species j The magnetic scattering amplitudes p Q are related to the magnetic form factors f Q e2 P Q 52 94H Q 3 9 The Bragg intensities calculated in this way can be converted into a Bragg profile function in pre cisely the same manner as for nuclear scattering 3 2 3 Implementation The various keywords and required parameters are listed in section 4 1 above and are not repeated here The basic idea is that all spin related files run from a slightly different user specified stem to that used for the standard RMC files For example one might use mno_spin as the stem name for the spin files associated with mno cfg mno his etc There are a few additional points to note 1 The spin configurations given in the spin cfg file are normalis
81. erall format is fixed so the easiest way to produce this file is to use the crystal program supplied with RMCProfile A description of how to use this program is given later if however this does not meet your needs then use it to produce a template cfg file for your system and then modify this as you need to If you got this far you are probably pretty committed to using this rather antiquated way of doing things in preference to the friendly version 6 approach described earlier You have our respect at least if not our sympathy However it is worth giving you a warning at this point In order to preserve backwards compatibility with the classic mode there are all sorts of things in the RMCProfile code that only exist because of this and one day we might want to tidy up and get rid of this stuff Thus there might be a day when we have to give up support for the classic mode so perhaps now is the time to switch versions Why not use the dat 2config utility to convert your configuration files into the new v6 format whilst waiting for your classic jobs to run 4 5 3 The poly sf and fs files These three files are required since the flag to use a polyhedral restraint is set to true in the dat file and then restraint 4 has been specified At the moment there are 14 different types of polyhedral 60 97 RMCProfile Manual v6 4 6 4 6 UPGRADE TO V6 restraints available with different combinations of polyhedra For the
82. erform this operation but in such a case the user will need to do this for himself before running RMCP rofile using one of our tools We strongly rec ommend using this subordinate keyword In this case the is required because we plan to add a compul sory parameter gt END POINT End point of the data an integer gt FILENAME Filename containing the data gt FIT_TYPE Reserved for the function that is fitted the only option today is F Q gt FITTED_OFFSET If specified this instructs the program to fit the offset value provided for this set of data Default is not to fit gt FITTED_SCALE Instructs the program to fit a scale factor for the data Default is not to fit gt NO_CONSTANT_OFFSET Instructs the code that no offset is to be applied to the scattering data before fitting This is the default setting although not necessary this keyword can be useful as a record for the user 40 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES v NO_FITTED_OFFSET Instructs the program not to fit any offset value on the scattering data This is the default setting although not necessary this keyword can be useful as a record for the user v NO_FITTED_SCALE Instructs the program not to fit a scale factor for the scattering data This is the default setting although not necessary this keyword can be useful as a record for th
83. es or use the prepared files conv29p42rmc dat supplied You should reproduce at least one of these files to check you follow the procedure and know how the programs work Once you have produced all the data files copy them into the main SFe directory together with the sf6mcgr190k dat file which contains the Fourier transform of the F Q files namely the G r Once again the preparation of the G r data will not be described here since it is normally obtained during the preparation of the total scattering data 6 2 3 The RMCProfile files The next file to prepare is the main dat file this can be copied from the example in section 4 5 1 or from the rmc folder You should check that the names of the data files in the dat file match the names you have chosen Finally the file for the polyhedral constraint needs to be prepared and since the SFg molecules form a octahedron polyhedral restraint 4 can be used The poly file can be copied from the rmc folder or produced with your favourite text editor the appropriate format is describing in section 4 7 4 and the ideal S F bond should be set to 1 56A The sf and fs files can be produced using the neighbour_list program when asked for a maximum distance 86 97 RMCProfile Manual v6 4 6 6 3 EXAMPLE 2 SRTIO3 enter 1 9 since this is bigger than the nearest S F distance but not far enough to include the next nearest neighbours When producing the s f file the program s
84. exp_QiQl Experimental scattering data for dataset 1 Array hkl_recalculate Flag Y N to denote whether hkl array was recalculated Scalar Investigator Metadata item on the investigators Text Keywords Metadata keywords Text lattice_vectors Matrix of lattice vectors Matrix maximum_distances Maximum distances in distance windows Array maximum_moves Maximum move allowed per atom type Array minimum_distances Minimum distances in distance windows Array neutron_coeffs_PDF1 Neutron coefficients for PDF dataset 1 Array neutron_coeffs_SQl Neutron coefficients for scattering dataset 1 Array nnpdf Number of neutron PDF datasets Scalar nnsq Number of neutron scattering datasets Scalar number_avcoord_constraints Number of average coordination constraints Scalar number _coord_constraints Number of coordination constraints Scalar number_density Number density Scalar number_of_species Number of different atomic species Scalar numbers of_species Numbers of atoms of each type Array nxsq Number of X ray scattering datasets Scalar offset_flag Y N values to denote application of offsets to data Array offsets Constant offsets applied to data Array partiall Partial PDF for atom pair 1 Array Phase Metadata item on sample phase Text Pressure Metadata item on sample pressure Text print_period Number of steps between printing Scalar Q Array of scattering vectors for scattering data Array QiQ1 Partial iQ Q data for atom pair 1 Array x Array of distances used in PDF function
85. factor The user will need to provide either this keyword line or the FORM FACTOR FILE keyword line File containing the magnetic form factors The user will need to provide either this keyword line or the FORM_FACTOR keyword line Stem name for the files associated with magnetic spins List of atoms that have an associated magnetic spin It is essential that these atoms are the first atoms in the configuration file so that a list of non sequential atoms would be invalid 35 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES gt MAX_SPIN_MOVEMENT Parameter that gives the maximum rotation of the magnetic spin in any RMC step gt NO_VARY_SPIN_MOVE_RATE Do not vary the rate of the spin move relative to the atomic displacements Default is not to allow the spin move rate to vary if this keyword or the VARY_SP IN_MOVE_RATE keyword is not given gt SPIN_MOVE_RATE Rate at which the spins are moved relative to the atomic displacement moves A value of 0 5 means that the number of attempted spin moves will equal the number of atom displacement moves a value less than 0 5 means that there will be more atom displace ment moves than attempted spin moves gt VARY_SPIN_MOVE_RATE Allow the rate of the spin move relative to the atomic displacements to be varied during the simulation De fault is not to allow the spin move rate to vary if this keyword is not given N
86. files As with the main program most of these are standalone programs however some are supplied in an archive zip form In this case all the files in the folder need to be kept together and the program run from its own folder 2 2 Running RMCProfile 2 2 1 Input files RMCProfile requires a number of input files that are described in the following sections Some of them will have the same stem name but different extension tags For example if we were performing an RMC simulation on the disordered crystalline material KCN we might have the following input files optional unless stated otherwise KCN dat containing the key data required to control the RMC simulation compulsory section 4 1 KCN rmc6f or KCN rmc 6c containing the atomic configuration in fractional or cartesian coordi nates respectively If using classic format the file name to be used is KCN cfg and you also have the option to call this KCN rme3f if using Version 6 dat file with classic configuration format This file is compulsory unless KCN his6f or KCN his6c is present section 4 2 7 97 RMCProfile Manual v6 4 6 2 2 RUNNING RMCPROFILE KCN his6f or KCN his 6c contains the latest configuration and the pair distribution functions as generated by the most recent run and if this file is present it will be used in preference to KCN rmc6f or KCN rmc 6c If using the classic file format this file is called KCN his subsection 4 2 3 KCN bragg
87. full list of options and the files required please see the polyhedral restraints section below The st and fs files contain a list of neighbours for sulphur and fluorine respectively the neighbours file required their file extension and how they are produced is also described in the polyhedral restraints section below 4 6 v6 4 RMCProfile for classic and RMCA users how to upgrade Let s get straight to the point if you are tempted to stick with the classic version or even worse with RMCA we have one word of advice don t And to make the switch easy we have provided some tools to help you upgrade There are basically two things you have to change First is the dat file and second is the format of the configuration file Let s deal with the configuration file first We have created the data2config tool Subsection 5 2 1 to make this simple You start with a classic cfg file and run the command data2config rmc6f lt whatever gt cfg You answer a few questions and out pops the new format configuration file The key questions concern the types of atoms you have in the configuration and when asked about the supercell type 1 1 1 if you don t want to make the configuration larger data2config can do much more than this for you for example it will help you generate configurations from crystallographic CIF files Executing the command without arguments will give you a list of options For more information t
88. g New func tionality has been added together with the introduction of completely new input file formats At the present time RMCProfile can still handle classic version file formats but we strongly recommend that existing users switch to the new formats To help this switch we have provided a some new tools to perform the file conversion that are described in section 4 6 The aim of this manual is to explain the practical issues of how to run RMCProfile and to describe the various files you need and how to format them The theory on which the method is based is described in the Appendices Not least because we do not guarantee support for classic file formats for ever 6 97 RMCProfile Manual v6 4 6 CHAPTER 2 INSTALLING AND RUNNING RMCPROFILE Chapter 2 Installing and Running RMCProfile 2 1 Installation At this point it is important to note that RMCProfile is provided as a singe executable that is de signed to be run as a shell command otherwise known as the command line or prompt if you are are using a Windows computer Thus no special installation is required just put it somewhere you can easily access it eg in usr local bin or in a folder that is accessed from your com mand path if you are using Linux or a unix based system such as Mac OS X or somewhere like C rmcprofile if you are using a Windows computer There are various other programs supplied as tools to help with preparation and analysis of the RMCProfile
89. h set to search your current working directory then you need to use the command in the way that specifies the path i e as data2config The optional arguments all of which are prefaced with a hyphen are cssr write the configuration to a CSSR Daresbury Laboratory s Cambridge Structure Search and Retrieval file format file which can be read by the CrystalMaker crystal visualisation program This has the advantage that it provides an easy way to check that the configuration is what you expected it to be This flag is switched off if the input file is itself a CSSR file be cause the action would be to overwrite the file The output filename has the extension cssr dlpoly write DLPOLY coNnFIG file you get this conversion for free because it was easy to implement rmc3 write the classic RMC version 3 configuration file output filename has the extension cfg This flag is switched off if the input file is itself a cfg file because the action would be to overwrite the file rmc6f write RMC version 6f configuration file a properly annotated input file with the atoms in fractional coordinates The output filename has the extension rmc 6f rmc6c write RMC version 6c configuration file which has the same properties as the version 4f file except that the lattice and coordinates are given in cartesian coordinates units of A The output filename has the extension rmc 6c crystal writes a file in the format us
90. his looks very similar to the configuration file format Extensions to the configuration file are mostly the information concerned with the additional data for the histograms from which the pair distribution functions are calculated 52 97 RMCProfile Manual v6 4 6 4 3 EXPERIMENTAL DATA FILES Since this file is generated automatically by RMCProfile there is no need to describe some of the information as optional Note that if you generate this file from a previous version 3 his file eg using data2config there will be no means to generate the 4 integer indices at the end of each atom line and thus these will not be given merely replacing each integer by zero will not achieve very much the default is not to include them This file usually has a filename with extension his6f 4 2 4 Version 6c format histogram file This file is virtually identical to the his6f format but the atomic coordinates are given in Cartesian format units A The files have a name with extension his6c 4 3 Experimental data files The main experimental data whether the scattering or pair distribution function data all have the same basic formats Moreover unlike other files you are free to chose any names for these files because the names are provided within the main dat file However to avoid confusion you might like to use an extension that indicates the type of file such as or for a G r PDF file or sq for the neutron scattering S Q file
91. hould report that it has found an octahedra and that the average coordination number is 6 If this is not the case something is wrong with the cfg file You should now have all the files you need to run RMCProfile on this system as described at the start of section 4 5 To run the full refinement using a 10x 10x10 super cell will take many hours so if you dont want to wait this long check things run and that the x values start to reduce Once you are happy everything is working you can copy the final cfg file from the rmc folder to get an idea of a final set of fits 6 2 4 Other things to try Once you are happy that RMCProfile is correctly set up and you can get it running you might like to try one or more of these suggestions e Try producing a smaller configuration say 4x44 and the appropriate total scattering data This will run quicker and demonstrate the minimisation process although the config uration may not be big enough to give a good representation of the thermal distribution of atoms e Try fitting just a subset of the data i e just the Bragg profile or Bragg profile or g r etc Again this will run more quickly and once x seems to be approaching a minimum you could addanother data set back in e Try replacing the polyhedral restraint with a distance window constraint This should produce a very similar final configuration but will illustrate the different functionality e Obviously the best thing is to try you
92. ighting for this bond restraint and then the weighting for the tetrahedral angle restraint The zro file contains a list of oxygen neighbours around each zirconium atom and the ozr file contains a list of the zirconium neighbours around each oxygen atom Similarly the wo file contains a list of oxygen neighbours around each tungsten atom and the ow file contains a list of the tungsten neighbours around each oxygen atom All of these neighbour files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 9 The Na3PO restraint This restraint defines a configuration of unlinked tetrahedra formed from the second and third atoms in the configuration as the name suggests it was first used for studying the molecular crystal Na3PO To use this restraint option 9 needs to be specified in the dar file and poly po and op files supplied The poly file contains a title line which is ignored and the next line must contain the ideal P O bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the octahedral angle restraint e 300 The po file contains a list of oxygen neighbours around each phosphorous atom and the op file contains a list of the phos phorous neighbours around each oxygen atom both of these files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 10 The NaNO restraint
93. ile RMCProfile allows all the above functions to be used to describe both the form of the input data and the functions to be fitted and hence used in the output In addition RMCProfile also allows Qi Q and synonymously QF Q to be used as well Normalised functions are indicated by the use of the word normalised For clarification the data or fit types for the various functions to be used in the input data file are TNote that equation 21 in Keen which is equivalent to second line of this equation is missing the value of 1 in the term for Shorm Q ad 0 The spelling normalized works just as well 47 97 RMCProfile Manual v6 4 6 4 2 RMC VERSION 6 FORMAT CONFIGURATION FILES Function Input text Equation from Keen Equation here i Q i Q 25 4 6 F Q F Q 11 4 6 S Q S Q 4 9 Qi Q Qi Q QF Q OF Q inorm Q i Q normalised 4 19 Frorm Q F Q normalised 4 19 Snorm Q S Q normalised 19 4 19 G r G r 10 4 2 4 7 G r Gr r 4 4 D r D x 26 4 11 T r Zei 27 4 12 Gnorm r G r normalised 4 15 Ghorm G r normalised 16 4 15 Dnorm r D r normalised 4 16 Thorm r T r normalised 4 16 4 2 RMC Version 6 format configuration files Version 6 of RMCProfile not only brings a new data format but it also brings several new formats for configuration files described generically as Version 6 format files whi
94. imulation with the bonds extension When this file exists the data contained within it will supersede the bonds data provided in the input file This is a good thing since often the bonds are established on a nicely ordered structure with no fluctuations that are hard for an automatic method to detect If you don t want to use an existing bonds file then rename or delete it A typical example has the form Metadata file type Bonds file for RMC simulation Metadata creation date 12 08 2009 Metadata material ZnC4 Number of atoms 10 Number of bonds 2 1 Zn 0 2 Zn 0 3 Cl SE pe lt snip gt 10 C 2 GE ok tThis might not work at low temperature because this discussion ignores the effect of quantum zero point motions in which case it might be necessary to use a higher temperature The lt snip gt lines replace similar data removed for the sake of brevity 13 97 RMCProfile Manual v6 4 6 3 1 INTERATOMIC POTENTIALS I Zon 2 ez 3 C 3 4C 6C 10 C 4 2 20 ee Es FSC sz 9 Cy A SE 2 ee 1 Z0 3 d CG 2 2 Ll Zn lt snip gt 9 C 2s 2 Sege 10 C 2 sz L SZmrz 1 The structure of this file is important The Metadata lines are important to link this file with the actual simulation but will be ignored by RMCProfile They are their for your benefit so dont delete them The two lines containing the number of atoms and number of bonds are important and must be
95. information no_ features suppresses requests for v6 features rmca use when you have an RMCA input file and disregard all following options old poly lt number gt use when the data file uses the old polyhedral input and give the key number of the polyhedral restraint old bragg lt resolution type gt use when the data file uses the old bragg input style without defining the type of resolution function and give the type of resolution function Email contact details can be obtained from http web me com dove_family martin contact html 80 97 RMCProfile Manual v6 4 6 5 2 TOOLS no magnetism use when data file doesn t include magnetism no_swap use when the data file doesn t include swapping You are unlikely to want to use the last two options but you may be tempted to avoid the use of the metadata facility Whilst properly annotating your data may be a slight irritation at the time if you are in a hurry cutting corners with metadata is both careless and reckless How many times have you put something down carelessly in a hurry and then spent longer looking for it than the time it would have taken to put it somewhere sensible Similarly sensible people exploit metadata facilities to the full and you would like us to think you are sensible surely The bottom line is that you should use the metadata features we have provided 5 2 3 crystal This program is an alternative to data2config for the generation of a st
96. information contained within Appendices how to install and run the RMCProfile program and how to prepare the input files The manual contains a number of examples with a couple of tutorials RMCProfile is still a work in progress and we have not yet reached the stage where next versions are just minor iterations from previous versions You will quickly appreciate that this manual reflects this fact in particular with the juxtaposition of two types of file formats v6 and classic This manual is copyright by the program authors and developers 1 2 Introduction the what is and why of the Reverse Monte Carlo method 1 2 1 The what is in a nutshell The Reverse Monte Carlo RMC method 1 will give you a unique view of the atomic structure of matter that is derived directly from experimental data The mainstream usage of RMC is to analyse neutron and x ray total scattering data from disordered materials which are materials for which other probes can only give limited data Examples include liquids and amorphous materials which provided the original motivation for the development of the RMC method magnetically disordered But because this is a work in progress regrettably there will be some things that are not yet properly documented 2 97 RMCProfile Manual v6 4 6 1 2 WHAT AND WHY OF RMC materials and crystals with significant thermal disorder rotational disorder of molecular groups and site occupan
97. ing peaks to build models that give you information about the atomic structure that extends to distances further than the first 3 peaks in the PDF Now is a good time to add a caveat A sharp peak in the PDF will tell you three main things First the position of the peak will tell you about the average bond length between the two atoms it represents and secondly its width will tell you about the temporal and spatial variations in the bond length which may arise from thermal fluctuations Thirdly the integral of the peak will tell you how many neighbours a single atom has Let us illustrate this with the case of silica chemical formula SiO The first peak at a distance of around 1 6 A corresponds to the Si O bond Its integral gives an average coordination number of 4 The obvious interpretation is that each Si atom has 4 O neighbours exactly as found in all ambient pressure crystal structures containing Si and O However the integral of the peak in the PDF only tells you about the average coordination number and an average value of 4 neighbours does not exclude the possibility that there are large numbers of Si atoms with 3 and 5 O neighbours And if you leave RMC to its own devices it will generate configurations with 3 and 5 neighbours In light of this it can often be advantageous to add additional constraints to the RMC method based on other experimental knowledge such as the constraint that all Si atoms will prefer to have 4 O neigh
98. is listed one per line The next line contains either y or n to tell RMCProfile whether to re calculate the Bragg scattering from the cfg each time the program is started This should always be set to y except when debugging runs and the time taken for the program to initialise is an issue Finally the sigma weight for the Bragg profile is supplied 59 97 RMCProfile Manual v6 4 6 4 5 RMCPROFILE VERSION 3 FILES The next line in the dat file is logical to determine if RMCProfile will convolute the neutron F Q data with its profile function This is only useful for time of flight neutron data and at the moment is at the experimental stage So for now it should be set to false and will not be described further here It will hopefully be a functioning option in the next release of the program and if you are interested in this option please email me The next line tells RMCProfile if it should calculate the magnetic scattering if the system being studied has a magnetic component In the example here the system is not magnetic so it is set to false the various options for magnetic systems will be discussed in the magnetic scattering section below once it has been completed The last two lines in the dat file tell RMCProfile the probability of swap moves and if not zero whether to auto tune this probability If the probability is not zero then the next line contains the two atom types that are to be swapped In the example
99. istance for each atom pair as in the dat file e ordered as the partials eg 1 1 1 2 1 3 2 2 2 3 3 3 for a system of three atom types and the second line has the furthest away distance in the same format Once run RMCProfile will then write a neigh file containing all the neighbour lists being used and a neighlog file containing a history of what has been done If you want to change the linkage or the configuration of atoms then the neigh file should be deleted before running RMCProfile again This will shortly change and it will become possible to include the data described here in the Version 6 dat file 26 97 RMCProfile Manual v6 4 6 CHAPTER 4 INPUT FILES Chapter 4 Input Files 4 1 RMCProfile version 6 input files 4 1 1 Introduction Version 6 of RMCProfile introduces some new input file formats which we recommend should be used in preference to the classic formats described later The main data files particularly the files containing the scattering data and the pair distribution function data so far remain the same as in the classic version but the main dat file and the configuration file have more transparent and more flexible formats and hence are easier both to create and analyse The histogram files also have new formats Actually by using the data2config program described in a later chapter on tools users will never need to create the configuration file by hand 4 1 2 The main dat
100. it cell rather that the configuration supercell and it is the supercell integers than enable RMCProfile to know how to set up the Bragg peaks 4 4 1a The optional hk1 file RMCProfile will calculate the Bragg profile for all Bragg peaks for d spacings down to a minimum value and for h k values up to a maximum value These limiting values are provided in a file with extension hk1 which will have the form The first line gives the minimum value of the d spacing and the remaining three lines give the limiting values of h k and respectively This file is not necessary if either of the gt DMIN or gt QMIN subordinate keywords are supplied within the keyword block under the BRAGG keyword RMCP rofile will compute the Bragg intensities for all reflections including those that are supposed to be systematically absent due to symmetry Whilst in a crystal structure refinement program this might be considered to be a waste of time in RMCProfile this is useful because it acts to ensure that the data drive the configuration into the appropriate long range symmetry rather than any symmetry being imposed from the outset 4 4 2 The bragg back and inst files 4 4 2a bragg file The Bragg scattering data is contained within a file with extension bragg It has the format appropriate for time of flight diffractometers an example being 1818 2 6 7798 274 9949 Sample data file 4 983635 4
101. its countable chi2_dof 43 5586 cmlUnits dimensionless chisq Pre emlUnits dimensionless chisq 2468 cmlUnits dimensionless chisq Ki emlUnits dimensionless Partial PDF functions em Abscissa rmcprofile riunits A Partial S Q functions Abscissa rmeprofile Q units invAng PDF total 110 W rmeprofile calculatedTotalPDF units mmeprofile experimentalTotalPDFiunits dimensionless m mmcprofile differencePDF units dimensionless J f Ay Ww 50 100 Abscissa rmeprofile rlunits Angstrom PDF total en Abscissa rmcprofile riunits Angstrom D r or I r r Number of neutron data sets Number of neutron reciprocal space data sets M Number of neutron total intensity data sets whether S Q i Q or Qi Q Numbers of species Numbers of atoms of each type Numbers of atoms of each type in order of atoms in the configuration number_density definition to be supplied Number of different i 9 g LEIG Created using ccViz by Toby White lt iow uszia me uk gt See CMLComp for more information Figure 5 4 Portion of the XHTML file generated by ceviz showing the data plots Each plot can be opened or closed using the Show Hide buttons Selecting a portion of a plot will give a magnified view summon t number_of_species c rmcprofile config ag3cocn6 xml The specific task from this command is to extract the number of species from the XML file here the example is called ag3cocn6 x
102. ive changes to the atomic configuration are proposed at random and then tested to see whether they improve or degrade the agreement that computed properties have with experiment data If the proposed change improves the agreement with data it is accepted and the algorithm moves forward one cycle in which a subsequent random change is proposed On the other hand if the proposed change degrades the agreement with data a probability algorithm is used to determine whether to accept or reject the proposed change By accepting what appear to be bad changes prevents the method getting stuck in a state whereby the agreement with experiment can no longer be improved even though there may be other configurations that are better Thus the Monte Carlo method enables you to explore a wide range of possible configurations The Monte Carlo method is based on statistical thermodynamics which means that there are good reasons to expect it to produce configurations that are in best agreement with data Thus the RMC method is a computer simulation approach but it differs from traditional simulations in that it is driven by experimental data rather than from parameterised equations There is a huge world wide industry in using models of atomic forces to construct models of disordered materials where experimental data are used at the outset to tune the models and at the end to validate the model through comparison between data and predictions but the actual modelling s
103. ive plot is given in Fig 3 5 The key difference with the previous fit e before refinement of the magnetic structure is that the 111 magnetic peak is now well modelled Note that our refinement only involved moving the magnetic moments all the atom positions remain the same so it really is the magnetic structure that accounts for this peak S Q o 5 10 15 20 25 Q A 1 Figure 3 5 A typical equilibrium RMC fit to neutron scattering data for MnO Before looking at the actual spin configuration we are going to set up RMCProfile to produce a series of equilibrium configurations This will help us produce smoother distribution functions by increasing sample size Again we need to amend the mno dat file this time changing false number of configurations to collect 500 step for printing 5 L Time limit step for saving to true number of configurations to collect 500 step for printing 10 5 Time limit step for saving Again we run RMCProfile using the command rmcprofile mno but this time it will save a copy of the configuration file after every 500 generated moves numbering the files sequentially In order to generate 50 new configurations we will need to leave the program to run for approximately 10 minutes 23 97 RMCProfile Manual v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING Meanwhile what we really want to do is to see what the newly refined magnetic structure looks like We will
104. l v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING Figure 3 2 The antiferromagnetic structure of MnO Mn and O atoms are shown as large light grey and small dark grey spheres respectively e000 X mnoeye Figure 3 3 The RMC starting configuration as seen in ATOMEYE using default colouring left and with Mn atoms coloured by the initial spin directions right then a new file mnoeye clr is produced which tells ATOMEYE how to colour each atom Re launching ATOMEYE via atomeye bat mnoeye cfg shows the same configuration as we saw previously but the O atoms are now coloured grey and the Mn atoms are coloured according to the spin orientations in mno_spin cfg A typical view is shown in Fig 3 3 The main point is that things look quite random It is instructive to see what the diffraction pattern looks like when calculated from this combination of atomistic and spin configurations and how it differs from the experimental data The RMcProfile parameter file mno dat is set up ready to be used for this magnetic refinement The experimental data are stored within the file mno_10k_sq dat and we are using a Q range of approximately 0 lt Q lt 25A These data have already been convoluted with a box function of width 8 88 A which is half the box size of our configuration Running the program using the command rmcprofile mno 21 97 RMCProfile Manual v6 4 6 3 2 MAGNETIC STRUCTURE MODELLING we obtain th
105. ld be used to produce the neighbour files required if a polyhedral restraint is being used Again it is run on the command file and will request the information required The output should be given the extension described in the relevant restraint section above and should have the same stem name as the other RMCProfile run files 5 2 9 neighbour list two This program is the same as the neighbour_list program apart from the feature that two sur rounding atoms can be supplied at the same time as required by some of the polyhedral restraints 5 2 10 rmc_to_atomeye This program can be used to convert RMCProfile configurations into the correct format to be displayed by the atomeye program described below It is run on the command line and asks for the information required 5 2 11 basic_x_server As the name suggests this program provides a basic X server to enable the graphical programs supplied with RMCProfile to function on a Windows computer It is supplied zipped in a folder and should be unpacked and stored in its own folder This is because it is actually a collection of programs from the cygwin distribution www cygwin com To run the program double click the 83 97 RMCProfile Manual v6 4 6 5 2 TOOLS rmc_startX bat file Windows security may ask for confirmation to run the program since it provides a service that other programs can access so please say yes to running it A command prompt window will appear and will rem
106. lecule on the corner of the unit cell and one in the centre However this average structure puts the fluorine atoms of neighbouring molecules too close together so on a local level the system tries to minimise the contact distance of these fluorine atoms by rotation of the octahedral molecules So the system is termed a frustrated system with fluorine fluorine repulsion driving the motion of the molecules With the data supplied you should be able to start with the ideal ordered structure and use RMCProfile to model the local deviation within the long range average BCC structure 85 97 RMCProfile Manual v6 4 6 6 2 EXAMPLE 1 SFg 6 2 1 The GSAS refinement As with most RMCProfile modelling the process actually starts with a GSAS refinement A rea sonable GSAS refinement is contained in the gsas folder and can be used to supply RMCProfile with all the information required to model the Bragg profile It also contains a cfgcom file with the BCC cell written out in P1 symmetry At the moment do not have a simple program to go from the GSAS atom positions to this P1 cell however GSAS supplies all the information required and it is a good exercise to try with your own system to ensure you start with a good understanding of the long range average structure To extract the rest of the information RMCProfile needs run the get_gsas_bragg program on the EXP file and select histogram 3 to be extracted for fitting with RMCprofile At this poi
107. ller in dices h k and This is not yet implemented but will be available soon The use of this subordinate key word will replace the need for the hk1 file gt NO_RECALCULATE Do not recalculate the list of reflections to use but use the ones provided in the hk1s file by a previous run This is the default setting although not neces sary this keyword can be useful as a record for the user gt QMAX Give the maximum value of Q to be used in the anal ysis of the Bragg diffraction data Users can use the DMIN subordinate keyword instead The use of this subordinate keyword will replace the need for the hk1 file 33 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES gt RECALCULATE Recalculate the list of reflections to use The default setting is not to recalculate gt SUPERCELL Three numbers to denote the supercell of the basic unit cell used to generate the atomic configuration This information can also be in the rm f file instead of here gt WEIGHT Parameter to weight the contribution of the Bragg pro file to the Monte Carlo simulation CML gt CCVIZ Instructs the code to run the ccviz program that con verts the xml file to an xhtml file The parameter gives the path and name of the ccviz program Exam ples are ccviz if the program is in the same lo cation as you are running RMCProfile from and use local bin ccviz if you are running ccviz from a sp
108. ly be transformed to other representations including XHTML This is exploited in the ccViz tool that will be described below and which is bundled with RMCProfile A second application called summon enables extraction of information from an XML file without having to scroll through the file These are supplied with the RMCProfile package both require Python to be available on the computer being used and both work from the command line CML within RMCP rofile has been enabled through Toby White s FoX package We note here that the incorporation of CML within RMCProfile is still new and any changes or additions can easily be added on request We anticipate shortly adding the opportunity to include CML representation of the atomic configurations The CML files generated by RMCProfile have the stem name with the xml extension We now describe two tools that exploit the use of CML to the user s advantage 5 1 2 The ccViz tool ccViz is a python program written by Toby White that will produce and information centric report in XTHML format i e a report that can be read using a web browser from CML files that follow a standard document model ccViz is run as a standard shell command with the name of the CML XML file as the argument as per this example ccViz filename xml It transforms the XML file to an XHTML file with the same root name that can be viewed with a modern web browser we recommend Safari for the mac and wind
109. ly the units are not interpreted default units are Angstroms Requires text that allows the user to attach a one line note about the specific simulation For example you could add a note to say that this is a test of one of several trial configurations This is used for metadata and is not compulsory Requires a number that indicates a version for the format of the saved configuration file At the present time this is line is not required but is reserved for future use Requires time period in minutes between sav ing the configuration Gives a flag to sort the atoms in in the input configuration for version 6 configuration files into the order of atom type Is useful when the generator program doesn t do this Default is not to sort Introduces a block of subordinate keywords that provide information about the atom swapping facility Default is to not use this swapping if this keyword is not provided Requires text to denote the temperature of the material being studied This is used for meta data and is not compulsory Units are not parsed Requires time limit in minutes for the job Requires text to act as a title for the run This is used for metadata and is not compulsory 32 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES XRAY_RECIPROCAL_SPACE_DATA Introduces a block of data concerning a set of neutron scattering data Text can follow the but will be ignored This keyword must b
110. m atom both of these files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 4 The SFe restraint This restraint defines a configuration of unlinked octahedra formed from the first two atoms in the configuration as the name suggests it was first used for studying the molecular crystal SFg To use this restraint option 4 needs to be specified in the dat file and poly sfand fs files supplied 63 97 RMCProfile Manual v6 4 6 4 7 POLYHEDRAL RESTRAINTS The poly file contains a title line which is ignored and the next line must contain the ideal Gr bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the octahedral angle restraint e 300 The s file contains a list of fluorine neighbours around each sulphur atom and the fs file contains a list of the sulphur neighbours around each fluorine atom both of these files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 5 The AIPO restraint This restraint defines a network of linked tetrahedra formed from the first three atoms in the con figuration as the name suggests it was first used for phases of aluminium phosphate This differs from the SiO restraint in that the network consists of tetrahedra of two sizes one for the AlO and one for PO To use this restraint option 5 needs to be specifi
111. m which it is easy to generate a file in png or gif format v6 4 4 Bug fixes only v6 4 2 1 The ability to add molecular constraints specifically bond stretching and bond bending The details are documented in the manual Version 6 3 v6 3 5 1 Fixed the input of NEUTRON COEFFICIENTS for the case where the list does not run over two lines the previous version allowed the list to run over more than the first line but didn t check for the case where it didn t 2 Added the CcV1zZ subordinate keyword to the CML keyword block allowing rmcprofile to automatically generate the xhtml file from the xml file There are certain requirements for this to work 3 Added the CSSR subordinate keyword to the FLAGS keyword block This allows automatic creation of a CSSR file for easy viewing in CrystalMaker 4 Added some missing code from the output section which had forgotten needed to be done Problem was that the code was printing out PDFs and scattering functions that differed from what was being requested Fixed some bugs on the way Tracked down the causes of occasional bus errors segmentation faults Added data_type and fit_type to the xml file output D N O A Tweaked some of the output messages 94 97 RMCProfile Manual v6 4 6 7 4 CHANGE LOG v6 3 3 1 2 3 4 5 Some small bug fixes eg getting the wrong name for the new configuration Completed the writing of his6f files I hadn
112. m1 in the user s directory The first parameter i e the one following is a keyword that denotes the property to be extracted The keywords are defined as XPath 73 97 RMCProfile Manual v6 4 6 5 1 VERSION 6 ANALYSIS TOOLS expressions in the file called rmcprofile config which in the example command is found in the same directory as the XML file In case you want to know but you don t actually need to know this specific case appears in rmcprofile config as the set of lines number_of_species type scalar xpath cml parameterList cml parameter dictRef rmcprofile number_of_species The last two lines are actually on the same line in the file in several of the following examples we have to allow single lines to flow over two You can see how the XPath instruction relates to the parameter number_of_species in the example XML file shown in Figure 5 2 The keyword is the word in square brackets in the first line The result of this example invocation of the summon command is number_of_species 4 This example is probably not per se a particularly useful use of the summon command because the user is likely to already knows how many atomic species there are but it is illustrative A more useful command of this kind might be to ask about the atom list and the number of atoms of each type This would have the form summon t atoms t numbers_of_species c rmcprofile config ag3cocn
113. me will be lost if the program or the computer crashes and how often the results are updated Setting this number too low will put a heavy work load on the machines hard disk typically for long runs 60 minutes is a good value to use On the following line the type and number of data sets to be used are defined Currently three types of data are supported neutron G r neutron total scattering i Q and x ray total scattering The file format is described in the RMCA manual and for the time being only a single x ray data set is allowed and up to five neutron G r and i Q data sets The information on the following lines in the dat files depends on the data specified in the previous line For each G r data set the following information is specified the filename of the data the first and last data points to be used a constant to be subtracted from the data the Faber Zimmer partial weighting factors Le the components of Y c b the sigma weighting of the data and a logical determining whether RMCProfile should rescale the data to give the best fit The same information is required for each neutron or x ray i Q data set but also an additional logical is required to define whether RMCProfile should calculate an offset of the data to give the best fit With all data types these rescaling and offset options should not normally be used only when the fit seems to have a scale problem should this option be used and then only so the program ca
114. meters note that summon help or summon h will provide a summary of the required parameters 72 97 RMCProfile Manual v6 4 6 5 1 VERSION 6 ANALYSIS TOOLS Don rmcprofile Output nitial Metadata v IER Mat Tucker D GE mg Dave Keen Andrew Goodwin Qun Hui Martin Dove Code n pame bied le e Code e Code pabicatin eist KN JC A 1088 0953 8984 19 33 335218 Code version le version ue SS L i version with keyword driven input fileand CML output E Sg SE Eo sep ne DS Sa SC ENT jata n oa collected August 2007 Keywords Ee G Ra Comment inement without peak broad 5 D e Andrew Goodwin and Matt Tui in Input Parameters gt Initial System gt Main Body of Simulation v rmcprofile summary Step 144815 v swapstried 92422 cmlUnits countable cht dei 43 5586 cmlUnits dimensionless chisq 52 5687 cmlUnits dimensionless chisq 44 2468 cmlUnits dimensionless chisa 0 0097 cmlUnits dimensionless L Ee Created using ccViz by Toby White lt tow uszia me uk gt See CML Comp for more information Figure 5 3 Top of the XHTML file generated by ccviz showing the initial metadata in expanded form the link to the input parameters in collapsed view and the output form a single step in the simulation By moving the mouse cursor over any parameter will bring up the corresponding dictionary definition 200 Output rmcprofile Output rmcprofile summary Step 144815 v swapstried 92422 cmlUn
115. n assess the rescaling required The data should be corrected before continuing with RMCProfile refinements The next two lines in the dat file define the number of coordination constraints and number of average coordination constraints These tend not to be used for crystalline system so are set to zero in the example given above and will not be discussed here If you would like to use them please refer to the RMCA manual The next two lines define the polyhedral restraint option first a logical tells RMCProfile whether to use a restraint and only if this is set to t rue then the following line contains the number of the restraint type to use The allowed values and addition files required are described in the restraints section below The next seven lines in the example dat file define the Bragg profile fitting options The first line is a logical indicating whether to fit the Bragg profile If this were set to false then the follow six lines would be omitted Here it is set to t rue so it is followed by the code for GSAS profile function to be used At the moment only time of flight functions 2 and 3 are supported so gsas2 or gsas3 More profile functions will be adding in the next release of RMCProfile The following line defines the number of unit cells in each direction within the RMCProfile super cell This is explained in more detail in the following cfg section Then the chemical symbol for each atomic species in the configuration
116. n Or Ltr 7 16 jk YB Y bjb sin Qr Orp 7 17 j jzk where we separate the terms involving the same atoms the self terms and those involving inter ference between different atoms We can express the equation using pair distribution functions rather than perform a summation over all atom pairs We define gmn r dr as the probability of finding a pair of atoms of types m and n with separation between r and r dr This function will have peaks corresponding to specific sets of interatomic distances For example in a material containing SiO tetrahedra there will be a peak corresponding to the Si O bond at 1 6 A and a peak corresponding to the O O bond at 2 3 A Each partial g r will be zero for all r below the shortest interatomic distances and will tend to a value of 1 at large r Thus we can rewrite Q as mg Q Il K Get IO So 7 18 m sin Qr Qr Q po E Cmenbmbn xr gmr 1 dr 7 19 m n 0 where Cm and cn are the proportions of atoms of type m and n respectively and p is the number density S is determined by the average density and gives scattering only in the experimentally inaccessible limit Q gt 0 91 97 RMCProfile Manual v6 4 6 7 3 RMC METHOD 7 3 Appendix C A primer on the Reverse Monte Carlo method The main task of the Reverse Monte Carlo method is to generate configurations of atoms from which computed properties most closely match experimental measurements with the prim
117. n distribution functions 3 1 6a Histogram file RMCProfile produces histograms of the number of bonds over the non uniform grid of 6 and a polar coordinates defined using the convention used in the physics community This file is given a name of the form lt name gt bondodf_n where lt name gt is the root name of the RMC simulation and n corresponds to the bond number It is important to note that this file is no more than a dump of the numbers of bonds that lie within the bit of solid angle defined by and and is not normalised for the size of the solid angle The grid is in uniform steps of A0 and Ad with grid size of 40 x 80 cells 3 1 66 PPM plot file By using the gt PLOT subordinate keyword RMCProfile will produce data in a form suitable for plotting as a stereographic projection as per this example The file is produced in the Portable PixMap format with name lt name gt bondplot_n ppm To convert to a more standard format such as png jpg gif tiff eps or pdf one option is to install a tool such aS Imagemagick To produce the image from Imagemagick execute the following shell command convert transparent black lt name gt ppm lt name gt lt extension gt Note that the mathematics community switches the meanings of these symbols here gives the angle a vector makes with the z axis 0 lt 6 lt 180 and gives the angle that the vector is rotated about the z axis 0 lt lt 360
118. n file contains a list of nitrogren neighbours around each carbon atom and the nc file contains a list of the carbon neighbours around each nitrogen atom both of these files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 12 The AgCN restraint This restraint defines a configuration of atoms linked in a chain structured formed from the first three atom types in the configuration as the name suggests it was first used for studying the molecular crystal AgCN To use this restraint option 12 needs to be specified in the dat file and poly agc cag cn nc nag and agn files supplied The poly file contains a title line which is ignored and the next line must contain the ideal Ag C bond distance to be used and the weighting for this bond restraint e 100 The following line must contain the ideal CN bond distance to be used and the weighting for this bond restraint The next line must contain the ideal N Ag bond distance to be used and the weighting for this bond restraint The agc file contains a list of carbon neighbours around each silver atom and the cag file contains a list of the silver neighbours around each carbon atom The cn file contains a list of nitrogren neighbours around each carbon atom and the nc file contains a list of the carbon neighbours around each nitrogen atom The nag file contains a list of silver neighbours around each nitrogen atom and the
119. nt of Qi Q It is also important to appreciate that it is necessary to have an absolute measurement of Qi Q if the resultant D r is to be interpreted quantitatively It is essential that all sources of addi tional scattering and all sources of signal attenuation can be independently determined and taken into account in the treatment of the data Wright 1993 Howe et al 1989 Dove et al 2002 It should be noted at this stage that there is a confusion in the literature in that different authors use different sets of symbols for the quantities discussed in this article including the use of G r 90 97 RMCProfile Manual v6 4 6 7 2 ISOTROPIC AVERAGING for what we have called D r This is a long standing historic problem Keen 2001 gives a good comparison of the different ways of labelling the fundamental quantities 7 2 Appendix B Isotropic averaging of the scattering function In this appendix we derive the equation for the scattering of radiation from an isotropic material This means that we assume that any interatomic vector r is found for all orientations which in turn means that we need to average over all relative orientations of r and Q We write rk rj rkl Q Q and x cos 9 and calculate the orientational average for one vector as 1 Za nr exp iQ rj rx a do f sin 6 d8 exp Qrj Cos d 7 13 i 5 f SPliArkx dx 7 14 8 sin Qrix On 7 15 Thus for all atoms we obtain S Q bjbk Si
120. nt you should have five files for RMCProfile in the gsas folder namely the bragg back inst hkl and cfgcom files Copy all of these files out of the gsas folder into the main folder using a common stem name i e sf6_190k bragg etc Now in the main SFe folder run the crystal program and enter the information in the cfgcom file or use the pipe command i e crystal lt sf6_190k cfgcom This should produce a 10x10x10 supercell of the BCC structure that will be saved in a file called sf6_190k cfg 6 2 2 The total scattering data The next stage is to prepare the total scattering data for RMCProfile How to collect and produce total scattering data is beyond the scope of this simple example and so will not be covered here The data folder contains three F Q files from three of the detector banks of the GEM diffractometer at ISIS It is quite common to combine these into one data set but here have left them separate to illustrate RMCProfile can fit many F Q data sets simultaneously The data is scaled from 1 to 0 so need to be multiplied by 0 27593 the sum of the neutron partial scattering factors to be suitable for RMCProfile The data also need to be convolved with the RMCProfile configuration box function to enable a fair fitting comparison Both of these operations can be performed using the convol_norm_new program For a 10x10x10 super cell the truncation distance is 29 42 so you can run the program to produce the new fil
121. ntains a list of nitrogren neighbours around each car bon atom and the nc file contains a list of the carbon neighbours around each nitrogen atom 66 97 RMCProfile Manual v6 4 6 4 7 POLYHEDRAL RESTRAINTS Most of these neighbour files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 however the zncn file should be produced using the neighbour_list_two program since both carbon and nitrogen atoms need to be specified as neighbours 4 7 14 The CFs restraint This restraint defines a configuration of unlinked C4Fg molecules formed from the first two atom types in the configuration This is a very specific restraint that defines a molecule of four carbon atoms arranged in a square with two fluorine atoms attached to each corner Only bond distance restraints are applied to hold the molecule together To use this restraint option 14 needs to be specified in the dat file and poly cc cf and fc files supplied The poly file contains a title line which is ignored and the next line must contain the ideal C F bond distance to be used and the weighting for the bond restraints e 100 and then the next line contains the ideal C C bond distance to be used The cc file contains a list of carbon neighbours around each carbon atom the cf file contains a list of the fluorine neighbours around each carbon atom and the fc file contains a list of the carbon neighbours around each fluorin
122. o change some of the Ca site labels by Mg and use this CSSR file as the input file for a second run of data2config designed to create a supercell If your disorder involves vacancies then replace some of the atom labels by the Va symbol 5 2 1e Further developments data2config has been written in a way that should make expansion of its functionality relatively easy For example different types of input file should be easy to add e g from other Rietveld structure output codes Moreover we have plans for added functionality such as the ability to convert hexagonal lattices to the corresponding non primitive orthogonal lattice Finally being a new tool there is a strong chance that there will be bugs in the code Bugs can easily be fixed by sending the code author a brief report by email and the input file that triggered a problem Similarly requests for new features can be sent to the author 5 2 2 rmc326 The rmc326 tool is provided to enable you to produce version 6 data files from old files in the classic format The tool is used as a shell command in the manner of rmc326 o lt Name of output data file gt options file to convert The tool will ask a few questions and then produce the basis of a version 6 data file to which you can add other features that are not found in the classic version The options are no metadata suppresses requests for metadata no atoms suppresses requests for atom
123. oodwin M T Dove M G Tucker and D A Keen MnO spin wave dispersion curves from neutron powder diffraction Physical Review B 75 art no 075423 2007 19 A L Goodwin S A T Redfern M T Dove D A Keen M G Tucker Ferroelectric nanoscale domains and the 905 K phase transition in SrSnO3 A neutron total scattering study Physical Review B 76 art no 174114 11 pp 2007 97 97
124. or these elements are 5 922 2 49 6 646 and 9 36 fm respectively Thus if the neutron coefficients are given in the input file the example line would be Z EUTRON_COEFFICIENTS 1 2329 0 3859 5 5347 7 7948325 0 0302 0 8661 1 219725 6 2113 17 495595 12 3201 fm where clearly the first value by way of example is equal to 5 922 3 16 and the second value is equal to 5 922 x2 49x3 16 Note that the list of values is allowed to span more than one line Also note that RMCProfile actually uses the default units for the scattering lengths of 10714m rather than fm 10 15 m and the classic mode input file would therefore require the input values to be lower than this example by a factor of 100 The program can detect which of the two units is being used although providing the units as fm 2 or as 10 28 m 2 is useful As noted above if this keyword is not provided RMCProfile will calculate all the values of the co efficients from default values of the neutron coherent scattering lengths and the calculated number concentrations For many applications this will be exactly what is required But consider the case 43 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES where you have data from samples with different isotopes Then each data set will require a differ ent set of neutron coefficients In this case you are able to use the gt NEUTRON COEFFICIENTS subordinate keyword within any
125. orien tations while keeping atom positions constant or proceeding with a dual refinement From experience a spin move rate of about 0 2 seems to work well in the latter approach Wu The value entered as the input parameter MAX_SP IN MOVEMENT is the variable omax described above In practice a value of about 0 1 seems to work well but it is important to keep an eye on the number of accepted spin moves and to adjust this value accordingly During its periodic updates to screen the program will allow the user to assess how many spin moves are accepted also relative to the number of displacement moves if these are allowed additional information comes from the change in x for each spin move which gives the user an idea of how strongly the data are driving magnetic structure refinement 3 2 4 Example refinement of magnetic structure in MnO Introduction This exercise focusses on the use of RMCProfile to refine magnetic structure in magnetic materials Just as RMC can be used to refine the crystal structure of a material in terms of the positions of atoms in a large supercell we can refine magnetic structures in terms of the orientations of spins in similar atomistic configurations One of the advantages of an RMC approach to magnetic structure refinement is that it is often possible to solve the magnetic structure even when starting from a completely random ensemble of spin orientations The example we will work through concerns the
126. ows platforms or Firefox for mac windows and linux platforms Older browsers or modern browsers that do not conform to FoX reference nttp uszla me uk space about 3http www apple com safari 4 nttp www mozilla com firefox 69 97 VERSION 6 ANALYSIS TOOLS 5 1 RMCProfile Manual v6 4 6 suood e Jo oWeIed pue eyepejoW ou DuuwOous o INdjno TWX STTFOTAOWNY Ue O ped Su OY WOJ SEIN UG an lt TeTeCOS gt 7 lt OTGequnNod STUNT us Si LE UD Die Ooiinau Jo ASsquny sweu bsu eTtyorzdowz Joy oOtp As jouezed gt lt zeqjewered gt ep zeqTeos gt lt SUOT OUNT lt ZeTe0S gt Z7 lt eTGeIUNOD sytuATWO s4tuN lt SUOTAOUNF nzobequt psx sedAjeq lt q4stTrejeuered gt lt ZeTeOS gt Z 3000000007T97 G lt yOuW S4tunTWoO sytun Teer xdz edALeqep lt AqtTSsuep AZequnNn seweu AQTsusep AZequnu seTtzyorzdo lt Aezze gt 8ZLT 8ZLI 882 798 lt ueTAequNOS sqtuATWO situn zrebe qu lt Setoeds Jo szequnn eweu setooeds Jo szequnu eTtyzomrdo lt Aezie gt N 32 OD by lt ySSeTUOCTSUSUTP Sq4TUATWO Ssqtun butzqs psx edAzeqep u y r79q4TW lt SedAq wo jy eweu swoje seTtgorzdo lt ZeTeOSs gt p lt buy sqtuqtTwo sytun lt Ssetoeds Jo 7equnn Seweu SsetToeds Jo Asqunu etTtjyorzdo lt u OOS u 7404974009 T psx edAlejep upa WT JOYMIOTP Zo ECK ZTS W TTSP ubu 9ZTs Ae WI FJOYIOTP Ao jouezed gt lt zejew nu2ebsqut psx edAje iep IeT
127. pG r 4 12 J The link between equations 4 11 and 4 7 should be clear The interesting point is that D r is the transform of the function Qi Q so often these two functions are considered together In these two functions the data are scaled by r and Q to give increased weighting to the high r and high Q parts of the data respectively This can be useful when viewing effects beyond the first peaks not least because it is often these effects that are particularly interesting The new PDF functions have limiting values 2 Dir gt 0 4rrp x di D r 0 4 13 j and 2 T r 0 0 Tirol dato P di 4 14 i 4 1 7d Normalised functions RMCProfile also allows the use of normalised functions For the PDFs we can defined these as Gnorm P av Del gt Ghom aw Den 4 15 2 2 Dnorm r D r 4rp Eee gt Thorm r T r 4rp Eee 4 16 with limiting values Gnorm r 0 1 S Gnermlf gt oo 0 Ghorm N 0 0 S Geet gt oo 1 4 17 and Dnorm r 0 r Dnorm f gt 00 O Thorm r 0 0 Thorm f gt cc r 4 18 Normalised scattering functions can be defined as 46 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES 2 inorm Q Fnorm Q IO 3 ob Snorm Q S Q x on 4 19 j j with limiting cases inorm Q 0 1 S inorm Q oo 0 2 4 20 Shorm Q 0 1 Cobi x d S Shorm Q gt oo 1 J J 4 1 7e Implementation within RMCProf
128. pins ppm to 24 mno_spins ppm Finally we combine these into a single animated gif with convert delay 20 loop 0 _mno_spins ppm mno_spins gif The animation can then be viewed in a web browser Further notes Other methods of analysing the RMC output include the generation of spin spin correlation func tions which measure the the degree of correlation between spin orientations as a function of dis tance Also we can extract some information about the spin excitations i e the magnons from the sharpness of the peaks in these correlation functions 25 97 RMCProfile Manual v6 4 6 3 3 DISTANCE WINDOW CONSTRAINTS 3 3 Distance window constraints The distance window constraint is an extension of the standard closest approach constraint in RMC In addition to specifying the closest two atom types can come you can also specify the furthest away two atom types are allowed to move apart In this way you define windows or config uration space in which the atoms are allowed to move When RMCProfile is first run a neighbour list of all the atoms that fit within the distance windows is generated and then remains the same unless deleted This means that the window sizes can be expanded or reduced but the atoms being constrained stays the same To use the distance windows constraint you do not need to change anything in the dat De Instead a dw file must be present This file contains two lines the first specifies the closest approach d
129. poly file contains a title line which is ignored and the next line must contain the ideal Zr O bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the octahedral angle restraint Le 300 The following line must contain the ideal TO bond distance to be used the weighting for this bond restraint and then the weighting for the octahedral angle restraint The zro file contains a list of oxygen neighbours around each zirconium atom and the ozr file contains a list of the zirconium neighbours around each oxygen atom Similarly the tio file contains a list of oxygen neighbours around each titanium atom and the oti file contains a list of the titanium neighbours around each oxygen atom All of these neighbour files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 7 The ZrP207 restraint This restraint defines a network of linked octahedra and tetrahedra formed from the first three atoms in the configuration as the name suggests it was first used for phases of ZrP207 To use this restraint option 7 needs to be specified in the dat file and poly zro ozr po and op files supplied The poly file contains a title line which is ignored and the next line must contain the ideal Zr O bond distance to be used the weighting for this bond restraint e 100 and 64 97 RMCProfile Manual v6 4 6 4 7 POLYHEDRAL RESTRAINTS then th
130. r own data if possible and just use the dat file as a template 6 3 Example 2 SrTiO Strontium titanate has the ABO perovskite structure and as such its crystal structure is made up of a network of corner sharing TiOg octahedral with strontium atoms in the interstices The example data and files supplied are from the GEM diffractometer at ISIS and were collected at 5K At this temperature the crystal structure is tetragonal with the octahdera tilted from their ideal positions in the cubic high temperature structure With the data supplied in the three folders gsas data and rmc you should be able to start with the ideal ordered structure and use RMCProfile to model the local deviation within the long range average tetragonal structure Unlike SFe this system does not have a high level of local disorder so the final configuration will be quite ordered in comparison The procedure required to run RMCProfile on this data is the same as described in section 6 2 but obviously substituting the SrTiOg files where required 87 97 RMCProfile Manual v6 4 6 CHAPTER 7 APPENDICES Chapter 7 Appendices 7 1 Appendix A Total scattering The phrase total scattering experiment refers to a measurement of the scattering of radiation by matter that covers all scattering vectors i e all values of sin 6 A and includes scattering with all possible changes of energy of the radiation It therefore encompasses elastic scattering such as from Bragg pe
131. res technique in Rietveld refinement Part of the reason for including as large a range of experimental data as possible in the RMC analysis is associated with the fact that the RMC method is effectively a method based in statistical mechanics As a result an RMC simulation will evolve to maximise the amount of disorder entropy in the configurations Thus the RMC simulation will give the most disordered atomic configurations that are consistent with the experimental data There may be a range of configurations that match the data with different degrees of disorder Only by maximising the range of experimental data can this problem be minimised 7 4 Change log Version 6 4 v6 4 6 1 Preparation work for v6 5 particularly with regards to handling per point errors on the data 2 Ability to read directly data files generated by the Gudrun data reduction and transformation package 3 Ability to read supercell information from the rmc6f file 93 97 RMCProfile Manual v6 4 6 7 4 CHANGE LOG 4 Ability to read the range of d spacings from the dat file and for the code to generate the range of h k values of the Bragg peaks used in the analysis of the diffraction data thereby removing the requirement for a separate hk1 file 5 Some internal workings to avoid array dimension overflow associated with the Bragg analysis v6 4 5 1 You can now automatically generate a ppm file from the bond orientation distribution function fro
132. rest neighbours etc The closest approach constraint is a powerful constraint and caution should be used to ensure the cut offs are not set too high as this may prevent the atoms moving enough to produce a true representation of the structure On the next line the r spacing to be used for histogram calculation is supplied this number should be the same as the r spacing of any G r data supplied Then a value of true or false is supplied to define whether to use the move out option This should be avoided for crystalline systems where the starting configuration should not have atoms that violate the closest approach cut offs It has been left in to be consistent with the forerunner RMCA program and for use with amorphous systems The next logical defines whether a configuration should be written at each print summary cycle This can be used to collect many configurations once a suitable equilibrium has been reached It can also be used to collect configuration up to equilibrium for movie making purposes 58 97 RMCProfile Manual v6 4 6 4 5 RMCPROFILE VERSION 3 FILES The number of generated moves between each print summary statements is then supplied This is not the same as accepted moves since these depend on the data weighting and other constraints Then next two numbers are the total run time and time between saves in minutes The last number determines how often RMCProfile saves a copy of the files this will determine how much ti
133. rom the Cygwin distribution called basic_X_server and this should be sufficient for the RMCProfile tools If you use Mac OS X or Linux Unix you are already set and ready to go 5 2 1 data2config This program will enable you to create a configuration file for RMCP rofile in any of the acceptable formats starting from a number of popular crystal structure files Examples of the types of input starting files include the cif and tb1 files known to crystallographers and outputs include the classic generation 3 configuration files which we do not recommend and the nicer version 75 97 RMCProfile Manual v6 4 6 5 2 TOOLS Table 5 1 Default list of summon keywords for RMCProfile output XML files Keyword Description of data Data type atoms List of atom types Array Bragg_background Coefficients for background function in Bragg profile Array Bragg_profile_type Bragg profile function used Scalar Bragg_weighting Weight applied to Bragg profile fitting Scalar close_approach Closest approaches allowed in simulation Array Comment Metadata comment Text DataNote Metadata note about data Text diff Bragg Difference between fitted and experiment Bragg profile Array diff _PDF1 Difference between fitted and experiment PDF 1 Array diff QiQ1 Difference between fitted and experiment scattering function 1 Array dSpacing d spacing for Bragg profile Array exp_Bragg Experimental Bragg profile data Array exp_PDF1 Experimental total PDF for dataset 1 Array
134. s 2 Na 0 0 0 0 0 0 C1 0 5 0 0 0 0 There are basically three blocks of data one specifying the unit cell dimensions one providing the minimum amount of symmetry information required to generate the whole crystal and one containing the list of atoms in the basis with atomic symbol and fractional coordinates The blocks can be in any order and the blank lines are not required On the other hand the numbers of symmetry operators or atoms are required as are the lines giving the keywords 5 2 10 Warning Users should be warned that in making the generation of configurations easy data2config also makes it easy for a lack of care to lead to problems further down the line In particular if your input file reflects a disordered structure for example one with partially occupied sites the disorder will 79 97 RMCProfile Manual v6 4 6 5 2 TOOLS not be handled automatically by data2config This should not come as a Surprise RMCProfile can simulate atomic site disorder but will only do so with real discrete atoms and vacancies and not using fractions of atoms as given by partial site occupancies One way to handle site disorder would be to generate a single unit cell with some artificial structure for example if you have Ca and Mg disordered over a single site merely call this site Ca with full occupancy for now Run data2config to generate a CSSR file containing single unit cell with several sites Then edit the configuration t
135. s Array renorm_flag Y N values to denote automatic data renormalisation Array RMC_Bragg Fitted Bragg profile Array RMC_PDF1 Fitted PDF function for dataset 1 Array RMC_QiQ1 Fitted scattering function for dataset 1 Array RMCNote Metadata note about the RMC simulation Text save_period Time between configuration saves Scalar supercell Multiplication of three unit cell edges to create configuration Array Temperature Metadata item on sample temperature Text time_limit Time limit set for job Scalar weights Relative weights for each dataset Array Use numbers 2 3 etc for subsequent datasets SEA RMCProfile Manual v6 4 6 5 2 TOOLS 6 configuration files using either fractional or orthogonal atomic coordinates data2config is designed to make this stage as easy as possible requiring very little effort from you as the user If you prefer tools that gratuitously give you extra work then we can recommend the crystal program that is described later Not only will data2config create new configuration files from starting crystal structures but it will also allow you to convert existing classic version 3 configuration and histogram files into the new version 6 format thereby helping you to gain maximum advantage from RMCProfile version 6 5 2 1a Command syntax The data2config program is run in the command or shell window by typing a command of the form data2config optional arguments filename If you don t have your pat
136. s they are read but ifthe Number of atoms line is not given RMCProfile will presume that the set of atom lines will be the last lines in the configuration file It will be assumed that Version 6f configuration files will have names with a rmc6f extension We have provided the data2config tool to allow users to generate this file from a number of different types of crystal structure files such as those produced by the GSAS Rietveld refinement program or standard CIF files data2config also allows you to convert classic format configura tion files into the Version 6f format 50 97 RMCProfile Manual v6 4 6 4 2 RMC VERSION 6 FORMAT CONFIGURATION FILES 4 2 2 Version 6c format configuration file This file format is very similar to that of Version 6f but uses Cartesian coordinates rather than fractional coordinates An example will illustrate the point Version 6c format configuration file etadata tile NaCl in a small box etadata owner Martin Dove etadata date 15 02 2009 etadata material Nacl etadata comment This is a test configuration etadata source Solid State Physics text book Number of moves generated 0 Number of moves tried 0 Number of moves accepted 0 Number of prior configuration saves 0 Number of atoms 64 Number density Ang 3 0 043656 Cell Ang deg 11 360000 11 360000 11 360000 90 000000 90 000000 90 000000 Lattice vectors Ang 11 360000 0 000000 0 000000 0 000000 11 36000
137. s will cause the program to convolve the reciprocal space data with a sinc function to model the effects of having a finite sample size Default is not to perform this operation but in such a case the user will need to do this for himself before running RMCProfile using one of our tools We strongly rec ommend using this subordinate keyword In this case the is required because we plan to add a compul sory parameter End point of the data an integer Filename containing the data 37 97 RMCProfile Manual v6 4 6 gt FIT_TYPE gt FITTED_OFFSET gt FITTED_SCALE gt GUDRUN gt NEUTRON_COEFFICIENTS gt NO_CONSTANT_OFFSET gt NO_FITTED_OFFSET gt NO_FITTED_SCALE gt START_POINT gt WEIGHT POTENTIALS 4 1 RMCPROFILE VERSION 6 INPUT FILES Gives the function that is fitted options are F Q QF Q i Q Qi Q or S Q together with the word normalised Or normalized for functions that are scaled by the neutron scattering coefficient X c cjb bj to give limiting values of 1 depending on the func tion This is explained in more detail in Section X If specified this instructs the program to fit the offset value provided for this set of data Default is not to fit Instructs the program to fit a scale factor for the scat tering data Default is not to fit If specified the data file was generated by the Gudrun data re
138. sense Hopefully a combination of providing upgrade tools and berating the reluctant will be sufficient to persuade you to switch before you run any more RMC jobs To switch will only take you a few minutes time that you will more than recoup once your job has run 4 7 Polyhedral restraints As mentioned above there are 14 different polyhedral restraints available in RMCProfile The large number is mainly due to the fact that each restraint is for a specific type of system rather than being a generic restraint definable by the user this has been done for simplicity of coding use of legacy code and for speed The 14 options are listed below and a brief description of each follows es SIOZ SrTiO CD SFe AIPO PZT ZrP207 ZrW20g Na3PO4 O o o NDT RF o hb ch NaNO ch KCN N AgCN 13 Zn CN o 14 C4Fe The names are derived from the first system to use that restraint but the restraint is suitable for any similar system For example the SiOz restraint defines a set of linked tetrahedra so could be used for any system where the first two atom types form a network of linked tetrahedra The weight for each restraint is set in the poly file The weightings are simple multipliers so a larger number means a heavier weighting These weightings should be chosen carefully such that 62 97 RMCProfile Manual v6 4 6 4 7 POLYHEDRAL RESTRAINTS the data weighting is always higher if this is not done
139. successive runs of RMCProfile However it is useful to understand the format of this file to enable it to be used for subsequent data analysis This file format is best illustrated with an example RMCProfile v6f intermediate histogram file etadata owner Martin Dove etadata date 17 02 2009 etadata material Ag3Co CN 6 etadata source Generated from RMC runs starting with our own GSAS structure Number of moves generated 92422 Number of moves tried 92343 Number of moves accepted 144815 Number of prior configuration saves 0 Number of atoms 4608 Number density Ang 3 0 052612 Cell Ang deg 42 150540 48 671252 42 692412 90 000000 90 000000 90 000000 Lattice vectors Ang 42 150540 0 000000 0 000000 0 000000 48 671252 0 000000 0 000000 0 000000 42 692412 Atoms fractional coordinates 1 Ag 0 082764 0 999551 0 080983 1 0 0 0 2 Ag 0 084347 0 998030 0 248759 2 0 0 0 3 Ag 0 083515 0 998656 0 415444 3 0 0 0 4 Ag 0 081875 0 000937 0 583213 4 0 0 0 4605 N 0 938087 0 920807 0 452244 13 5 5 5 4606 N 0 940870 0 914326 0 618485 14 5 5 5 4607 N 0 951886 0 912453 0 789664 15 5 5 5 4608 N 0 940857 0 927571 0 956517 16 5 5 5 Number of points in pair distribution functions 1053 Step size in pair distribution function 2 00000000000000004E 002 step AgAg AgN N N 1 0 0 0 2 0 0 0 3 0 0 0 172 85 71 47 173 88 68 45 174 84 95 34 175 117 70 42 176 112 90 47 177 93 78 25 178 96 74 56 179 70 71 58 180 77 73 55 In many ways t
140. t DATA_TYPE gt CONSTANT_OFFSET gt CONVOLVE gt END_POINT gt FILENAME 4 1 RMCPROFILE VERSION 6 INPUT FILES Requires list of neutron scattering coefficients prod ucts of scattering lengths and number concentrations for all atom pairs particular to this data set only The data are allowed to straddle several lines of the file Default units are 10 20 m The default values are cal culated by the code if this keyword is not given see section 4 1 6 Instructs the code that no offset is to be applied to the T r data before fitting This is the default setting although not necessary this keyword can be useful as a record for the user Instructs the program not to fit the offset value pro vided for this set of data This is the default setting although not necessary this keyword can be useful as a record for the user Start point of the data an integer Parameter that weights the data in the simulation Gives the type of data options are F Q QF Q i Q Qi Q or S Q together with the word normalised Or normalized for functions that are scaled by the neutron scattering coefficient X c c b b to give limiting values of 1 depending on the func tion This is explained in more detail in Section X If specified it allows the user to provide an offset that applies to the scattering data before fitting Default value is 0 0 if this keyword is not provided If specified thi
141. t and lt parameter gt tags with the following format lt parameterList gt lt parameter dictRef name gt lt item gt lt item gt lt parameter gt lt parameterList gt 68 97 RMCProfile Manual v6 4 6 5 1 VERSION 6 ANALYSIS TOOLS where in Figure 5 1 the quantity specified by lt item gt is either lt scalar gt or lt array gt depending on data type and there is specific information contained within the tags The examples in Figure 5 1 include parameters that are set by the user input such as the list of atom types and others that are deduced from the input file such as the number of data types or number of atomic species Note that each parameter item contains a dictRef a reference to a dictionary item describing the parameter and a name The data items are accompanied by a description of the units Figure 5 2 shows actual data generated These are contained within lt module gt tags which are defined for different tasks or roles The examples in Figure 5 2 illustrate two specific roles one called role step for step by step output the serial number gives the actual step number and another called role plottable which contains final graphs e g partial pair distribution func tions and comparison of data and calculated functions for plotting with the ccViz tool described below There are several applications that stem from using XML data representation In general terms XML files can easi
142. t site c An optional numerical atom label integer immediately after the atomic symbol given within square brackets This integer can have any value d Three fractional coordinate values Unlike Version 3 configuration files the assumption is that the origin of the box has coordinate 0 0 0 and that x y and z values range from 0 1 A single optional integer that is appropriate if the configuration is a supercell of a funda mental crystallographic unit cell In this case the integer will correspond to the atom in the crystallographic unit cell that this atom corresponds to Wu lt jes A set of three optional integers that are appropriate if the configuration is a supercell of a fundamental crystallographic unit cell In this case these integers denote the position of the origin of the unit cell containing this atom relative to the origin of the configuration with the origin cell denoted by integers 0 0 0 and for a supercell having dimensions Nx x Ny x Nz the three integers range in value from 0 Nx 1 0 Ny 1 and 0 Nz 1 respectively Note that if the optional integer giving the label of the atom in the origin cell is included previous input quantity these three integers must follow that integer 12 There are as many atoms lines as there are atoms There is no termination line If the number of atoms is given in the Number of atoms line the lines will be counted a
143. t way is to just type crystal on the command line and hit return assuming the program is in your path or the same folder as the command prompt window and then enter the information above Alternatively the information can be saved to a file say s 6_190k cfgcom and then run by typing crystal lt sf6 190k cfgcom and hitting return again it is a assumed here the sf 6_190k cfgcom is in the current directory or path Note that the data2config tool can both read and generate files in the format used by crystal Not entirely sure why 5 2 4 convol_norm_new This program is used to convolve the neutron structure factor data with the RMCProfile configura tion box size function This used to be necessary with all RMC methods to ensure a fair comparison of calculated to measured data but now the same task can be achieved directly within RMCProfile v6 However if you still prefer to use the classic mode this is one more task that you have to do convol_norm_new is run on the command line and it asks for the information required It also has options to multiple the data by a constant and subtract a constant in case the data needs to be rescaled for use with RMCProfile t And one more reason to decide to switch to v6 format files 82 97 RMCProfile Manual v6 4 6 5 2 TOOLS 5 2 5 data_rescale This program can be used to rescale data to make it suitable for RMCProfile even including adding a x offset if required For exampl
144. tage is divorced from experimental data The RMC method takes a radically different approach in that experimental data are used directly to drive the development of the model at all stages There are no equations or parameters that drive the model 1 2 2 The why in a nutshell Having briefly summarised the what is of RMC the chances are that you are now impatient to know more about the why Like many techniques RMC is not the sort of thing you can just dabble with and so you need to be convinced that the pay off is worthwhile tThis should be qualified by noting that later on we will see how addition of some equations can help guide the simulation to focus on the more interesting features 3 97 RMCProfile Manual v6 4 6 1 2 WHAT AND WHY OF RMC Let us go back to our first statement namely that RMC will give you a unique view of the atomic structure of matter and let us illustrate this by thinking about liquids and amorphous materials Their atomic structure is described by the pair distribution function PDF which is effectively a histogram of interatomic distances A typical PDF will contain a small number typically 1 3 sharp peaks at small distances followed by a structured distribution containing overlapping peaks on increasing distances The first peaks can tell you about the relative positions of a small group of less than 10 atoms but no more The RMC method enables you to exploit the data in the overlapp
145. the simulation moves us away from a purely data driven ap proach However we have found that there are cases where the use of interatomic potentials called polyhedral restraints in the classic version of RMCProfile have an important role For example small errors in the data can cause the configuration to distort locally and some form of restraint can be useful to minimise this effect Moreover the RMC method has no means to def initely associate any feature in the data with specific features in the configurations For example a peak with an area corresponding to a mean coordination number of 4 doesn t actually preclude the formation of structures with coordination numbers of 3 and 5 provided that the average remains as 4 Thus the use of potentials for restraints on the configuration can have a role in preventing bad things happening to the configuration which is not quite the same as forcing some desired behaviour In some cases particularly with molecular crystals the PDF at lower distances can be dominated by the contribution from intramolecular distances This may not be very helpful since there is often little of scientific interest in the shape of the molecule as compared to how separate molecules interact Using potentials is a way of enabling the simulation to place more emphasis on the interatomic contacts that are not included in the potential With proper weighting of the contribution of the potential with respect to
146. the weighting given to the agreement with data the role as a simple restraint works well Only when the data are under weighted will the potentials be the primary driving force in the simulation and a principle the relevant author subscribes to 10 97 RMCProfile Manual v6 4 6 3 1 INTERATOMIC POTENTIALS 3 1 2 The available interatomic potentials 3 1 2a Bond stretching potential We assume that the energy required to stretch a bond can be described using a Morse potential Ey D 1 exp a r 19 3 1 The function is written in this way so that the energy is zero at the origin as it is for simple polynomial expansions of the bond stretching energy Aside from the r parameter The Morse function has three adjustable parameters namely ro to specify the length of the bond D to specify the energy required to break the bond and a which plays a role in specifying the curvature of the potential energy function around the minimum Following the MM3 molecular mechanics force field model we set a 2 55 for all atom pairs We can write a simple expansion of the Morse potential to lowest order Em Da r fo 3 2 If you prefer to work with this type of quadratic expression but expressed in the following way Ew iktr n 3 3 the association between k D and a is clear We recommend the following realistic values for the parameters taken from the MM3 database units of D are eV units of pn are in A
147. then the restraint will become a constraint and the data will be ignored and the resulting configuration biased Please note none of the restraints support swapping moves of the atoms linked by the restraint at the moment This feature will be added in a later release of the program if required 4 7 1 The SiO restraint This restraint defines a network of linked tetrahedra formed from the first two atoms in the config uration as the name suggests it was first used for phases of silica To use this restraint option 1 needs to be specified in the dar file and poly sio and osi files supplied The poly file contains a title line which is ignored and the next line must contain the ideal Si O bond distance to be used the weighting for this bond restraint e 100 and then the weighting for the tetrahedral angle restraint e 300 The sio file contains a list of oxygen neighbours around each silicon atom and the osi file contains a list of the silicon neighbours around each oxygen atom both of these files should be generated using the neighbour_list program supplied with RMCProfile and described in section 5 2 4 7 2 The SrTiO restraint This restraint defines a network of linked octahedra formed from the first two atoms in the configura tion as the name suggests it was first used for studying strontium titanate Since the octahedra are formed from the first two atoms in the configuration it must be set up to actually represent TiO
148. thin the Bragg scattering and total scattering can be appreciated by considering the basic scattering equations The starting point is the static scattering function Q KQ p Eb exp Q Jo li 7 1 J where bj is the scattering factor for atom labelled j r is the instantaneous position of this atom and N is the number of atoms in the sample Q is the scattering vector defined as the change in wave vector of the neutron beam associated with the scattering process note that the wavelength of the 88 97 RMCProfile Manual v6 4 6 7 1 TOTAL SCATTERING scattered beam can change through the scattering process For coherent scattering i e where all atoms of the same type scatter the same way this can be rewritten as KQ E ByBx exp iQ ry si 7 2 jk where the overline represents the average over all atoms of the same type The main point of this equation is that it shows how the intensity of scattering is determined directly by the instantaneous distances between atom positions and does not directly contain information about the actual posi tions of individual atoms For periodically ordered systems the information about the positions of individual atoms is contained within the Bragg peaks The equation for Bragg scattering is 2 1 IBragg Q N A exp iQ rj 7 3 i If we consider an atom to have a mean position r we can write the average as exp iQ elt exp IQ 1j pe F exp IQ x dr 7 4
149. think it is very useful It was written by J Li at Ohio State University and can be used to display the RMCProfile configuration once it has been converted into the correct format using the rmc_to_atomeye program described above For a full description of the program and to download the latest version if required please go to http mt seas upenn edu Archive Graphics A The version supplied here requires an X server to be running and again all the files should be stored in the same folder i e c rmcprofile tools atomeye It can then be run in two ways the first way is on the command line by typing c rmcprofile tools atomeye atomeye bat lt lt atomeye file gt gt where atomeye file is replaced by the configuration converted by the pro gram rmc_to_atomeye i e rmcsf6_190k eyecfg again this assumes the program has been stored in c rmcprofile tools atomeye and if not the correct path should be specified the second way to run the program is to right click on the atomeye file i e rmcs 6_190k eyecfg then to select open with and then find and select the atomeye bat file A terminal window and a graphics window will then appear If you select the graphics window and press F1 then a help file will be displayed in the terminal widow For full instructions please look at the web address given above Actually we would recommend that you consider getting yourself a Linux or Mac OS X system
150. tun Teet xdjz edAleqep 99 Ty eZzTs LIIe gt lt Two gt wtOANgTr4UOO oOp suweu eIepeqou gt ow gt gt lt pOTTgOrgbberzgqeouerzesstp aeTtjgorzdows seyqotp Aqyzedoird gt lt n2T92990Td eT02 wTp S4TuAt lt nesqutod Z Uu TT bstyo e 29S gt T 0ZE9PO6LI PZP P lt uSSOTUOTSUSUTpP S9 lt uzsqutod Z Ou lt uTSqutod Z fUn usuotyouns 204 tTyoado TUNTUD us run H ET LTL bsty O eTtyzoardo lt eTnp lt ast TAqasedoid lt Aqazedoid gt WO SytTuN Teer xdj edAlejep JI Wt y JouRotp Ayrzedoid gt lt Aqizedoid gt eoi xdj edALeqep azepTeos gt ss JS Rotp Ayrzedoid gt lt Aqazedoid gt TunTWwo Ssytun Teer xdjz edAjejep Ieqeos gt ET LTL wer PDS gt T87098996S8GSE p lt ySSeTUOTSUSUTp S7 O eTtyzoado TUN TWO y S4 lt u FOP 7Z TU 98T ECKE EA EENS ELSE hale run H SET lor EN O eTtyzoado WI y souRotp Aqrzedoid gt lt Ayzedoid gt eoi xdj edALeqep zepTeos gt WT y soy Rotp Aqrzedoid gt lt Aqazedoid gt Two Sqtun z7ebequt psx edAleqjep rzepleos gt lt uP TI sdems wo qW eTITQ petaqasdems aT tyoado WT a jJoY qotp Ayazedoid gt lt astyAqszedor eTIedy STITF STNpow gt ow gt gt d gt lt deqs eT07 Azeumns eTtzordowsz FOYAOTP aGI8ppIua TETI SsS eTnpou gt 71 97 RMCProfile Manual v6 4 6 5 1 VERSI
151. um In the RMC method the experimental total scattering data corresponding to the values of y in the equation for x can be Qi Q or Dir In fact in our work we use both at the same time It is also possible to include additional data such as the Bragg scattering profile or XAFS data and to also include a contribution from the use of restraints Accordingly we write the RMC xy in the following form xBuc B 7 22 m where Sm 0 1 and we define a separate x for each set of data 92 97 RMCProfile Manual v6 4 6 7 4 CHANGE LOG no Ld Aas Qk Qlexp Q x 02 Q 7 23 xB E Deal Deel Wio 7 24 Xprotile z LE fie Felt ta 7 25 Lier ai of 7 26 XBs En wei at a 7 27 XB far LK e080 cos 6 7 28 The term Ce corresponds to the polyhedral constraints Keen 1997 1998 where f may be a bond length or bond angle with the required value obtained from the low r peaks in D r The profile term was introduced by ourselves for the study of crystalline materials Tucker et al 2001b 2002a 2002b The terms yZ and yg are the new molecular constraints where the parameters are designed to be realistic so that the weighting term is now related to the experiment temperature The function Iprofiie t describes the Bragg diffraction pattern Our work is mostly based on time of flight neutron sources SO kene a function of neutron flight time t This is the same x that is minimised by a least squa
152. units as or A in which case give the units as Ang Sample temperature in units of Kelvin or C in which case specify the units as K or C respectively The default units are K Note that this value will be over ridden by the value of sample temperature provided in the metadata input 39 97 RMCProfile Manual v6 4 6 4 1 RMCPROFILE VERSION 6 INPUT FILES gt NO_SWAP_TUNE Don t tune the swapping probability This is the default setting although not necessary this keyword can be useful as a record for the user gt SWAP_ATOMS List the numbers of atoms to be swapped gt SWAP_PROBABILITY Probability that a pair of atoms will attempt a swap A value of 0 5 means that the number of attempted swap moves will equal the number of atom dis placement moves a value less than 0 5 means that there will be more atom displacement moves than at tempted swap moves gt SWAP_TUNE Tune the swapping probability Default is not to tune XRAY_RECIPROCAL_SPACE_DATA gt DATA_TYPE Reserved for the type of data the only option today is KS gt CONSTANT_OFFSET If specified it allows the user to provide an offset that applies to the scattering data before fitting Default value is 0 0 if this keyword is not provided gt CONVOLVE If specified this will cause the program to convolve the reciprocal space data with a sinc function to model the effects of having a finite sample size Default is not to p
153. urn to subsection 5 2 1 To convert the dat file to the new v6 format we provide the rmc326 command subsection 5 2 2 You simply need to run the command rmc326 o lt newfile gt dat lt oldfile gt dat There are a few more options that you can find from running the command with no arguments or looking at subsection 5 2 2 Hopefully this makes switching to v6 4 as easy as possible In case you are still not sure here are some reasons to upgrade sooner than later e v6 files are designed to be easy to use whereas the classic and RMCA formats were designed with more or less little regard for the user e V6 files contain information metadata that will better enable you to keep track of your data e v6 formats make available all of the new features being introduced into RMCProfile which you can t access from the classic format files These include different data formats in tramolecular potentials use of XML output with the tools these makeavailable to you and any new developments we will be adding e We cannot guarantee that support for classic format files will continue for ever indeed when it becomes too much effort we will make a decision to stop supporting the classic format 61 97 RMCProfile Manual v6 4 6 4 7 POLYHEDRAL RESTRAINTS e And if you are still using RMCA you need to be aware that there is now no support for this code Indeed the source code for the later versions has disappeared e You know it makes
154. ways in which the format is quite flexible For example the order of the lines is completely arbitrary apart from the constraints on the use of the END line and the input is case independent The input files also reduce the need to provide redundant data whilst allowing you to do so if you wish You are also allowed to include blank lines 28 97 RMCProfile Manual v6 4 6 4 1 3 Major keywords 4 1 RMCPROFILE VERSION 6 INPUT FILES This is the first of two boring but essential and comprehensive sections of information associated with the input data file format We recommend that you skim read this now and return to it after you have seen an example given below Note that the word requires used in this list indicates the required parameters not that this keyword is actually required ATO MS AV ERAG E COORDI NAT ION CONSTRAINTS BRAGG CML COMMENT DATA FILE VERSION DATA NOTE Requires labels for the atoms in the configura tion file This keyword is not required when Ver sion 6 configuration files are being used can guess what this is supposed to do but don t know enough about this to be able to say what is needed Default is to not use this con straint if this keyword is not provided Introduces a block of subordinate keywords that provide information about the Bragg scattering data Do not include if you have no Bragg profile

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