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EPSR worked examples

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1. 1 0 391226E 01 0 300000E 03 0 000E 00 0 100E 00 0 100E 01 0 100E 01 0 100F 01 0 650E 02 6 BODOH ODO HHOH 0 000000E 00 0 000000E 00 0 000000E 00 1 e 1 5 2 0 108E 01 3 0 108E 01 4 0 108E 01 5 0 140E 01 6 0 190E 01 M 2 4 1 0 108E 01 3 0 176E 01 4 0 176E 01 5 0 203E 01 M 3 4 10 108E 01 2 0 176E 01 4 0 176E 01 5 0 203E 01 M 4 4 1 0 108E 01 2 0 176E 01 3 0 176E 01 5 0 203E 01 o 5 5 1 0 140E 01 6 0 976E 00 2 0 203E 01 3 0 203E 01 4 0 203E 01 H 6 2 5 0 976E 00 1 0 190E 01 1 C e f 0 39000E 00 0 37000E 01 0 12000E 02 0 00000E 00 0 00000E 00 M H 0 0 65000E 01 0 18000E 01 0 20000E 01 0 00000E 00 0 00000E 00 o o 0 0 58500E 00 0 30830E 01 0 16000E 02 0 72800E 00 0 00000E 00 24 H H 0 0 00000E 00 0 00000E 00 0 20000E 01 0 43100E 00 0 00000E 00 0 10000E 01 0 30000E 01 CCD O0O0OCTODOVO0CO0ODCDOO UGX ONO OOOO OUROO0D OO OD D 1 methanol 0 100000E 01 0 100000E O01 Note that 6 OUR IONNONUOUUUUERUONNONODUOUUEEOD 0 000000E 00 0 000000E 00 The molecule is placed at the centre of the box coordinates 0 0 0 il 5 2 0 108E 01 3 0 1089E 01 4 0 108E 01 5 0 1408 01 6 0 1 90R 01 M Z All of the atoms are also at the centre of the box ROT 5 1 3 2 3 4 Rotational axis is from atom 5 O to atom 1 C With 3 atoms dependent on this rotation atom 2 3 and 4 M The atom that comes second in the definition of the axis determines what group wi
2. LU The Orientational Correlation Function properly said is selected by setting 3 The meaning of what we are plotting now depends on how we have actually setup our initial axes on the molecules and an understanding of the Euler angles representation Quoting from the manual again A description of Euler angles can be found in a number of textbooks The definitions used here are based on Theory of Molecular Fluids Volume 1 Fundamentals C G Gray and K E Gubbins Oxford University Press 1984 which also gives an excellent account of the spherical harmonic functions The order of the rotations being used here to get to the final orientation is important The entity is first rotated by an amount about the initial z axis then by an amount 9 about the new y axis finally by an amount x about the revised z axis that is generated by the second rotation All rotations are in the direction of a clockwise screw along the positive axis They can also be performed in reverse order but rotating about the fixed laboratory axes throughout TODO It also requires a bit of graphic construction in order to build the image of our first reference molecule at the centre of the figure with the axes in the correct position with respect to what we have established in the SHARM dat input file Other graphical choices are available regarding colours and transparency of the image but not necessary The example below will help setting up a first att
3. Several atoms can be specified For the second axis it may not be possible to assign a set of atoms which lie along the specified axis so instead a vector is drawn from the centre of the molecule to the point defined by the set of specified atoms and the second axis is assumed to lie in the plane defined by the this vector and the first axis its precise direction is determined from the requirement that it must be orthogonal to the first axis The molecule as defined MUST have at least one plane of mirror symmetry and at least one of the mirror symmetry planes must be coincident with the z x plane If such a plane does not exist in the real molecule then mirror symmetry about the z x plane will be imposed on the estimated distribution functions and it likely they could be misleading Here follows an example of how to setup an input file that calculates the spherical harmonics coefficients setup input file gt File class sharm file extension SHARM dat File Not Found No files of extension SHARM dat found in directory C EPSR17 run met met__sharm No files selected Type the required filename with extension met setup_input_file gt Full filename C EPSR17 run met met_12_sharm met SHARM dat setup input file gt Problems with specified input file met SHARM dat will use default values Setup sharm gt Setup sharm gt fnameato Name of ato file fnameato lt undefined gt met Attempting to read file met ato minitc gt
4. 5 K 2 3 4 ic C 0 0 39000E 00 0 37000E 01 0 12000E 02 0 00000E 00 0 00000K 00 M H 0 0 65000E 01 0 18000E 01 0 20000E 01 0 00000E 00 0O 00000K 00 Oo O 0 0 58500E 00 0 30830E 01 0 16000E 02 0 72800E 00 0 00000K 00 H H 0 0 00000E 00 0 00000E 00 0 20000E 01 0 43100E 00 0 00000H 00 0 10000E 01 0 20000E 01 23976 1149980312 313375245 763635818 17267122452 2125952865 2104917671 809766993 699594297 1667287044 959103680 1057147157 643295378 1118800511 1410340799 1064918654 311045925 989545951 773664677 2116227401 1149980312 1979976970 447123753 1876842048 801051620 353008694 477082433 1432739048 1340056068 1664201980 44129405 1587877127 2137356202 409080103 1199357746 1 methanol 0 100000E 01 0 100000E O1 Note that C 1 5 2 0 10086E 01 3 0108EF0L 4 O 10EEFOL S Os 140 FOL 6 0 190E 01 M 2 Now the coordinates of each atom relative to the center of mass are different from zero and compatible with the bond distance i 0 50274E 00 0 28944E 00 0 24052E 00 tt 26 S This is the bond distance C aka atom1 is at 1 08A from atom 2 3 and 4 M etc Now we want to make a box with many methanol molecules using mixato EPSRshell gt mixato mixato gt How many ATO files do you want to mix 1 mixato gt Search for ato file 1 Filename methanol ato Type y to accept u to go back e to exit y minitc gt Following molecule types found ic 0 10000E 01 0 10000E 01 minitc gt Following molecule types found Le methanol 0 10000
5. A 0 03 fwhm OG Resolution width Q independent term 0 0 fwhmq 0 02 Resolution width Q dependent term 0 02 for SLS 1 1 means background subtraction is ON 0 means OFF Minimum value of Q used for potential fits 0 05 nrtype 5 Data type see User Manual for more details rshmin 0 7 Minimum radius A used for background subtraction szeros 00 Zero limit 0 means use first data point for Q 0 tweak 1 0 Scaling factor for this data set 1 0 efilereq 1 9 Requested energy amplitude for this data set 1 0 q At this point we actually match each dataset with its own wts file it s normally good to have them in some sort of logical order such as H D Fabio tus gmin 0 05 Minimum value of Q used for potential fits 0 05 data a NIMRODO0000045 mdcs01 nrtype 5 Data type see User Manual for more details rshmin OF Minimum radius A used for background subtraction szeros 0 0 Zero limit 0 means use first data point for Q 0 tweak 1 0 Scaling factor for this data set 1 0 efilereq 10 Requested energy amplitude for this data set 1 0 data Z NIMROD00000057 mdcs01 nrtype 5 Data type see User Manual for more details rshmin 0 7 Minimum radius A used for background subtraction szeros Q 0 Zero limit 0 means use first data point for Q 0 tweak 1 9 Scaling factor for this data set 1 0 efileregq 150 Requested energy amplitude for this data set 1 0 data 3 NIMROD00000050 mdcs01 nrtype 9 Data t
6. 0 q 18 Running EPSR MC only to equilibrate First off we just want to run a MC simulation without any refinement so we have to make sure that potfac is set to 0 As in the silica example we can run EPSR once by simply typing epsr at the in the EPSRshell prompt it then asks us for the inp file name To run EPSR more than once we can copy the run script we created for the silica to the water run directory change the file that epsr should run on in this example water_1000 EPSR inp and execute it using the command ss runscript txt at the EPSRshell Since this system contains many more atoms it will take a bit longer to run than the silica example After a while if we look at the energy p 14 in plot we see that it has dropped and is levelling off as the system relaxes The periodic spikes in the energy happen when the intramolecular coordinates are changed all at once to give the system enough intramolecular disorder C EPSR examples_rh water_2 water_3_mc_only water_1000 50 L 4 0 50 100 150 200 Iteration number If we look at the fit compared to the data sets p 7 we see that the fit is not that good since we have not added in the empirical potential yet 19 C EPSR examples_rh water_2 water_3_mc_only water_1000 3 5 0 5 10 15 20 QA Adding in empirical potential As described in the silica example we turn on refinement by changing some of the variables in the inp file must set pot
7. 0 16667E 00 Atomic fraction 1 Atomic fraction 0 50000E 00 0 16667E 00 2 Atomic fraction 3 Atomic fraction 4 0 16667E 00 no of molecules to read 1000 6000 4 10 changeato gt There are 4 types of atom in this file Atom type 1 has label C Atom type 2 has label M Atom type 3 has label O Atom type 4 has label H changeato gt 31 changeato gt bond Intra molecular bond lengths Type y to change bond n changeato gt label Atom labels Type y to change label n changeato gt density Density of this ato file density 0 089290015 changeato gt temp Temperature of this ato file temp 300 changeato gt stepmi Intramolecular translation step stepmi 1 02 changeato gt stepri Intramolecular rotation step stepri 1 e changeato gt Current data have not been saved Type lt CR gt to save or q to exit without saving changeato gt Current name of file is met ato changeato gt Writing to input file met ato changeato gt File met ato already exists Do you want to overwrite it y or n y The variable stepri has to be put at 1 if you want to turn on rotations of the rotational groups in the simulation Lines that require your input have been highlighted 32 Setup a simulation box flowchart Create a mol file for each molecule you want to put into the box plotato Number density and relative composition of the system Jmol Jmol 33 Sett
8. 0 203E 01 9 0 203E 01 4 1 0 108E 01 2 0 176E 01 3 0 176E 01 0 S 0 62257E 00 0 27662E 00 0 30857E 00 S 1 0 140E 01 6 0 976E 00 2 0 203 0 203E 01 H 6 0 59375E 00 0 11747E 01 0 62659E 01 2 5 0 976E 00 1 0 190E 01 1 ROT 5 1 3 2 S 4 6 0 000000E 00 0 000000E 00 0 000000E 00 0 000000E 00 2 S 1 E 2 0 108E 01 3 0 108E 01 4 0 108 0 190E 01 M 2 0 11533E 01 0 97934E 00 0 45225E 00 4 1 0 108E 01 3 0 176E 01 4 0 176E 01 M 3 0 12542E 01 0 38858E 00 0 67153E 00 4 1 0 108E 01 2 0 176E 01 4 0 176E 01 M 4 0 15029E 00 0 10603E 01 0 86880E 00 4 1 0 108E 01 2 0 176E 01 3 0 176E 01 O S 0 62257E 00 0 27662E 00 0 30857E 00 5 1 0 140E 01 6 0 976E 00 2 0 203E 01 0 203E 01 H 6 0 59375E 00 0 11747E 01 0 62659E 01 S 5 0 976E 00 1 0 190E 01 1 ROT S 1 3 2 3 4 ECG eLO Note that MOOD 0 406552E 02 0 300000E 03 We have 1000 molecules in the box Molecule 1 EPSR kindly counts them for us 6 0 000000E 00 0 000000E 00 Molecule 2 6 0 000000E 00 0 000000E 00 3 0 203401 0 000000 4 0 000000 E 00 E 00 All the molecules are at the origin and they all have the same orientation in space To randomize their positions and their orientations we run introtcluster 28 The molecules are now nicely scattered throughout the box but their intramolecular coordinates are all the same they all have the exact same bond length and internal angles so we give them some thermal disorder by running fmole
9. exactly runs Performing EPSR with one dataset requires 43 parameters to be set we are going to require more since we have three datasets Using the setup epsr command from EPSRshell it prompts you to set various variables It prompts for lots of different things to do with how EPSR works You can supply the filename when you call the command setup epsr lt filename base gt if the file does not exist then setup creates it with defaults The search command is useful for when asked for a file name as it can search for files of a given extension Many of the variables do not need to be altered and the defaults are fine After all the questions it creates a file with the extension EPSR inp which is the input file for the EPSR program Sometimes this is the best way to setup an inp file Often the easiest way of dealing with this is to get a basic inp file and then edit by hand this is faster than answering all the questions that the setup epsr command asks A new one can be created by running setup epsr giving the base for the filename in this case sio2 and then exiting e and saving The variables which have defaults have these written in the file and those that don t have defaults have their values flagged as lt undefined gt The key parameters in the inp file to change are fnameato fnamepcof ndata here this needs to be set to 1 since we have 1 dataset and then for each dataset we need to specify the datafile wts file and the nr
10. file to write the wts file to since selected H2O it produces a file called H2Otot wts 6 Finally it asks if the total data has been normalised or not here we select not 0 This procedure needs to be done for the other two samples D20 and HDO specifying the correct isotopes and their abundance and so as not to overwrite the previously made wts file a new file 17 basename has to be given In the case of the HDO file where there is a mixture of deuterium substituted hydrogen atoms it once you specify a fraction of isotopic substituted atoms epsrwts asks you about the fractions of each Making an inp file As with the silica example we use setup epsr passing the command water_1000 as the basename for the file to give us the basic inp file EPSRshell gt setup epsr water_1000 We exit by typing e and save the file A basic inp file is then created in this case it is called water_1000 EPSR inp Then we edit the file in a text editor ensuring that define the parameters fnameato fnamepcof ndata here ndata needs to be set to 3 since we have 3 datasets and then for each dataset we need to specify the datafile wts file and the nrtype here we have Gudrun histogram type so nrtype 5 for all files When we make the basic inp using setup epsr we only have the parameters for one dataset so we have to copy and paste the relevant parts twice to be able to define all 3 datasets The bottom part of the inp file should loo
11. run So now we can use this second window to examine how EPSR is running using the plot command see section 3 6 Make sure we have a plot_defaults txt file in the directory with the basename for the ato file set correctly in this case sio2 Look at the energy p 14 the S Q fits p 7 and their Fourier transform g r p 12 and see how they improve or not with time The top few lines of the plot_defaults txt file should now look like this plot_defaults Title of this file I 0 Lists available plot types sio2 File name to plot b Le 3 Block numbers to plot e g 12 5 9 6 P 27 Plot using the current or specified plot type npt 27 Number of types of plot Below is p 14 the energy of the system and we can see that the energy of the system decreases as the system relaxes Also show is p 7 which shows the fit to the data we can see that it is not very good but this is because the system is still at 10 000K C AEPSR examples_rh silica_with_silvia silica_3_mc only_equil_300K sio2 2000 F i i E 1000 a D L Block 1 4 1000 J 2000 5 3000 p J 0 50 100 150 200 250 300 350 Iteration number 12 C EPSR examples_rh silica_with_silvia silica_3_mc only_equil_300K sio2 1 5 1 F J 05 H S 4 o Ss nain 2 E al KT ae 0 5 L x as J F E 0 5 10 15 20 Q HIA Equilibration at 300K So next we change the temperature of the system to 300K using the changeato command
12. the input file and then we modify it 35 setup input file gt File class epsr file extension EPSR inp File Not Found No files of extension EPSR inp found in directory C EPSR17 run met met_7_ ts No files selected setup_input_ file gt Full filename C EPSR17 run met met_7_wts met EPSR inp setup input file gt Problems with specified input file met EPSR inp will use default values Setup epsr gt Current data have not been saved Setup epsr gt Current name of file is met EPSR inp Setup epsr gt Writing to input file met EPSR inp met EPSR inp met EPSR Title of this file feedback 0 8 Confidence factor should be lt 1 0 8 potfac 0 0 1 0 to enable potential refinement 0 0 to inhibit ereq 5 0 Overall requested energy amplitude overrules efilereq sizefactor 1 0 Multiplying factor for box dimension 1 0 nq 400 Number of Q values 400 qstep 0 05 Size of Q step 1 A 0 05 ireset 1 Sets the Empirical Potential to zero iinit it Sets accumulators to zero Recalculates r and Q 1 ntimes 5 Number of MC cycles between potential refinements 5 niter il Number of potential refinements befor Mites 1 nsumt i Number of iterations already accumulated 1 with reset intra 100 Number of molecule moves between molecule shakes 100 inter 5 Number of iterations in running averages 5 rho O 1 Atomic number density will be derived from ato file cellst 0 03 Size of r step
13. transparency of object 0 0 1 25 2 50 3 75 130 6 8 2 0 1 0 diffuse shine polish and contrast 15 35 rotation and elevation of viewing point deg 0 extra lines 0 cannot be set 0 extra text 0 cannot be set SHARM hO1 Here have a number of options that include the radius range want to consider for the plotting what variables do choose to plot human beings can visualise maximum 2 plus the radius but there are 6 in our physical system The radius for the SDF has to be determined from the corresponding g r in our case the O O g r e g am trying to look at correlations between methanol molecules from the hydroxyl oxygen point of view remember had chosen in the met SHARM dat file atom c O Central molecule list of centre atom types 47 atom s O Second molecule list of centre atom types From the gO O r it s clear that there is a first correlation peak between 2 and 3 3 Hence 2 0 S23 minimum and maximum radius of plot in the met plot3d txt file C EPSR17 run met met_12_sharm met 90 This is the standard setting for Spatial Density Function U use 11 and 12 1 or 0j 0 use nl and n2 1 or 0 use m2 1 or 0 vary thetal phil 1 thetam phim 2 thetam chim 3 LA O LA La Then need to make the puppet molecule picture at the centre of the box so that the reference frame attached to it is obvious from the picture For example 2 number of spheres at centr
14. 0 fmole asks for how many shakes you want to perform on the molecule and since our molecules in this case are very simple 1 iteration is sufficient And it asks for the frequency to update the neighbour list just type 0 here Complex molecules may require more This then prints some output detailing the iterations that fmole is running eventually returning the EPSRshell prompt fmole should also be run on si ato So now these two ato files have been altered with the atoms given coordinates Next we need to mix our two ato files to form the system of 250 silicon atoms and 500 oxygen atoms To do this we run mixato EPSRshell gt mixatoe mixato gt How many ATO files do you want to mix 2 Mixato gt Search for ato file 1 Filename o ato Type y to accept u to go back e to exit Y minitc gt Following molecule types found 10 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 10 o 0 10000E 01 0 10000E 01 2 118229 2 44592 no of molecules to read al 1 L 1 0 244592E 01 14 632776 0 06833973 Atomic fraction 1 0 10000E 01 no of molecules to read L 1 p p 1 new atom types in file C EPSR examples_ rh silica_with_silvia making_ato_an d_inp 2 o ato Atom type 1 has label O mixato gt How many of these molecules do you want in the mixture 500 mixato gt Search for ato file 2 Filename o ato Type y to accept u to go back e to exit Filename si ato Type y to accept u to go back e to exit mi
15. 67E 00 0 50000E 00 Atomic fraction 0 16667E 00 2 Atomic fraction 3 Atomic fraction 4 0 16667E 00 no of molecules to read 1000 6000 4 10 30 update atoz methanol ato fmole gt Iteration 97 Intramolecular energy 0 18956E 02 No of moves tried 6000 No of moves rejected 4497 fmole gt Iteration 98 Intramolecular energy 0 19084E 02 No of moves tried 6000 No of moves rejected 4522 fmole gt Iteration 99 Intramolecular energy 0 19046E 02 No of moves tried 6000 No of moves rejected 4481 Done fmole Note on rotational groups Now when mixing molecules with rotational groups e g methanol and molecules without e g water EPSR may switch off the option to rotate the groups It is always better to double check this and if necessary switch it back on using the changeato command setup input file gt File class changeato file extension ato Filename met ato Type y to accept u to go back e to exit y setup_input_file gt Full filename C EPSR17 run met met_6_fmole met ato setup input file gt Reading input file met ato setup input file gt Run name in input file is different from filename specified C EPSR17 run met met_6_fmole met ato minitc gt Following molecule types found Le 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 1g methanol 0 10000E 01 0 10000E 01 35 20844 40 6552 no of molecules to read 1000 6000 6000 4 0 406552E 02 67196 76 0 089290015
16. E 01 0 10000E 01 3 3881166 3 91226 no of molecules to read b 6 6 4 0 391226E 01 59 880188 0 10020009 Atomic fraction 1 0 16667E 00 Atomic fraction 2 0 50000E 00 Atomic fraction 3 0 16667E 00 Atomic fraction 4 0 16667E 00 no of molecules to read 1 6 4 10 4 new atom types in file C EPSR17 run met met_4 ato2mixato methanol ato Atom type 1 has label C Atom type 2 has label M Atom type 3 has label O Atom type 4 has label H mixato gt How many of these molecules do you want in the mixture 1000 mixato gt Give atomic number density per A 3 of mixture 0 08929 mixato gt Type name of file to put mixture in met met ato file after running mixato MOOD 0 406552E 02 0 300000E 03 0 000E 00 0 929E 00 0 100E 01 0 100E 01 0 100E 01 0 650E 02 6 BDE HHEH HOOD 0 000000E 00 0 000000E 00 0 000000E 00 L C 1 5 2 0 108E701 3 0 109EF01 4 0 108E 01 5 Q 140E 01 6 0 190E 01 M 2 2lIS3SE 01 0 97934E400 0245225 2115 4 1 0 10908E 01 3 0 1768 01 4 0 176E 01 amp 0 202801 M a 0 123942BE 01 O S8858H4 00 0 67133EF00 4 1 0 108E 01 2 0 17668E 01 4 0 176E 01 9 0 203E 01 M 4 0 15029E 00 0 10603E 01 0 86880 00 27 5 0 203840 E 01 0 000000 E 01 3 02203801 4 E 00 0 000000E 00 5 LDR 6 o G 203nt02 5
17. EPSR worked examples By Rowan Hargreaves and Silvia Imberti updated for EPSR18 on 12 May 2009 In this section we present a number of worked examples starting with initially quite simple examples working up to more complex ones Also the description given in the examples becomes briefer in the later examples to avoid repetition The general procedure followed in these worked examples 1 Set up the simulation build an initial configuration set up the weights files which describe the diffraction data and set up the input file which controls how EPSR runs 2 Run the simulation equilibrate the system s configuration using MC only then introduce the Empirical potential to the refinement and then accumulate data and finally 3 Analyse the results This tutorial has been written from a user point of view and tries and put together the actions needed to perform a simulation in the order in which they need to be performed For this reason it may be sometimes oversimplified and does not substitute the need to read the manual in order to understand precisely what it is that you are doing while running a certain sequence of programs A reference to the relevant section in the manual is given Set up for Windows There are many ways to run EPSR but here only one way will be explained so that you can get easily started Copy the EPSR18 folder under your C drive The bin folder contains the batch file needed to run EPSR the mol f
18. Following molecule types found LE 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 1 C methanol 0 26816E 00 0 79901E 02 35 20844 40 6552 no of molecules to read 1000 6000 6000 4 0 406552E 02 67196 76 0 089290015 Atomic fraction 1 0 16667E 00 Atomic fraction 2 0 50000E 00 Atomic fraction 3 0 16667E 00 Atomic fraction 4 0 16667E 00 no of molecules to read 1000 6000 4 10 There are 4 types of atom in this file Atom type 1 has label C Atom type 2 has label M 42 Atom type 3 has label O Atom type 4 has label H Setup sharm gt fnameato Name of ato file fnameato met ato Setup sharm gt nr Number of radius values max 200 r 100 5 Setup sharm gt rmax Maximum radius for spherical harmonic coefficients x 10 2 E Setup sharm gt nsumt Number of configurations already accumulated nsumt 0 Setup sharm gt ncoeffs Number of coefficients program calculates this ncoeffs 0 Setup sharm gt llvalues L1 values separated by spaces llvalues 012 3 4 Setup sharm gt l2values L2 values separated by spaces l2values 012 3 4 Setup sharm gt lvalues L values separated by spaces 12values 012 3 4 Setup sharm gt nlstep Step in N1 values nistep 1 Setup sharm gt n2step Step in N2 values n2step 1 Setup sharm gt atom c Central molecule list of centre atom types atom c O Setup sharm gt axiscl First axis definition f
19. R runs you can play carefully with these two files here a way that works consistently it is given so that you don t need to worry about it EPSR doesn t have a graphic interface yet and it is run through a DOS Windows which is something that was very common in the past but some people may not have seen before So for the young sic among you here are the basics The way it is recommended you should run EPSR is by opening an MS DOS prompt Start gt All Programs gt Accessories gt Command Prompt or equivalent It may be useful that you create a shortcut Another way to open a Command Prompt window is by selecting Run Start gt Run and typing cmd Now you can move to the run folder and create a new folder in which you will copy the files included in the startupfiles subfolder Microsoft Windows XP Version 5 1 2600 C Copyright 1985 2001 Microsoft Corp C Documents and Settings si67 CLRC gt d epsris8 run C EPSR18 run gt mkdir mynewsim C EPSR18 run gt 8opy Sar pup es neus startupfiles epsr bat startupfiles epsr sh startupfiles f0 WaasKirf dat startupfiles gnuatoms txt startupfiles gnubonds txt startupfiles plot_defaults txt startupfiles runepsr txt startupfiles runepsrbenz txt startupfiles system_commands txt startupfiles system_commands linux txt startupfiles system_commands windows txt 11 file s copied C EPSR18 run gt d myn wsim C EPSR18 run mynewsim gt diz Directory of C EPSR18 run my
20. about one particular molecule 2 a 750 750 plotato gt 2 components available for plotting 1 6 2 Si plotato gt Give number of components to plot and component numbers 2 12 plotato gt Number of classes read from gnuatoms txt 12 plotato gt Following atom classes will be plotted 10 2 Si plotato gt Min and max of plot 0 120000E 02 0 120000E 02 plotato gt For each new bond type two atom symbols minimum and maximum lengths of bond and radius of bond Type 0 0 0 0 O to end bond input or ste 0 0 0 0 for stereo pairs plotato gt 00000 plotato gt Total number of bonds read in 6 plotato gt Give overall scale factor on atom sizes plotato gt Give plot rotation about x and y deg 30 30 plotato allows you to select the ato file you want to view here I have cycled through the ato files by pressing return until get to sio2 ato and select it by typing y There are three different ways to view the ato file using GNUplot PGplot or JMol here select GNUplot by typing 1 Try all of them in order to see the difference The Jmol option is the last one implemented and it is probably the most user friendly Next select that want to plot all of the atoms option 1 and tell it to plot both components by typing 2 1 2 the first 2 means plot two components both oxygen and silicon atoms the 1 refers to the first component and the 2 refers to the second component We don t have any bonds in this system so
21. again While fmole on the single molecule is very quick this time it will take a lot longer as it has to do the same operation on many many molecules C EPSR17 run met met_6_introt2fmole met ato minitc gt Following molecule types found ic 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 1 C methanol 0 10000E 01 0 10000E 01 35 20844 40 6552 no of molecules to read 1000 6000 6000 4 0 406552E 02 67196 76 0 089290015 Atomic fraction 1 0 16667E 00 Atomic fraction 2 0 50000E 00 Atomic fraction 3 0 16667E 00 Atomic fraction 4 0 16667E 00 no of molecules to read 1000 6000 4 10 fmole gt makemole methanol 1 2 3 bond bond bond angle angle angle rot potential potential potential 29 potential temperature vibtemp density ecoredcore 39344 o w N B O R A w W N BH O R E R Q A KA KA 34 A 5 2 1 08 3 1 08 41 08 5 1 4 6 1 8965269 411 08 3 1 7615492 4 1 7615492 5 2 0309799 08 2 1 7615492 4 1 7615492 5 2 0309799 411 08 2 1 7615492 3 1 7615492 5 2 0309799 5 5 1 1 4 6 0 976 2 2 0309799 3 2 0309799 4 2 0309799 6 2 5 0 976 1 1 8965269 1 5 1 3234 4 c 1 M 3 o 2 H 4 minitc gt Following molecule types found ig 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 1 C methanol 0 10000E 01 0 10000E 01 35 20844 40 6552 no of molecules to read 1000 6000 6000 4 0 406552E 02 67196 76 0 089290015 Atomic fraction 1 0 166
22. atoms The most robust way to make an initial configuration of the system is to use the makemole command see section 4 3 To use makemole one must create a mol file to make an ato files for each atomic type here one for silicon and one for oxygen The mol file is a template file which can be created in a text editor but for speed it is often best to take a copy of one already known to work and alter it for the molecule we are trying to make In this case we have supplied a mol file for both oxygen and silicon o mol and si mol respectively In this case we are treated the two atomic types as molecules molecules of one atom and no bonds The mol files contain the potential parameters for the atoms First we run makemole on our two mol files For each file run on makemole creates two files a atm file and a ato file Below shows makemole being run on o mol the oxygen atom mol file EPSRshell gt makemol 6 mol 1 potential temperature vibtemp density ecoredcore i170 22 1 O 00 t701 FOR 0 1 EPSRshell gt This creates o ato and o atm and similarly running it on si mol creates si ato and si atm For now we are only concerned with the ato files The next stage of the process is to give the atoms some coordinates using the command fmole see section 4 4 EPSRshell gt Emole 6yato fmole gt Type the number of times to perform the shake 1 fmole gt Type the frequency to update the neighbour list 0
23. be per atom 1 or per molecule 2 i epsrwts gt The following components were found in this file Component no label atomic fraction chemical symbol 1 Ow 0 33333E 00 o 2 HW 0 66667E 00 H epsrwts gt How many samples 1 2 or 3 0 to quit 1 epsrwts gt Get the scattering lengths for all components in the sample epsrwts gt For component OW Type 0 for a natural isotope or mass number for a specific isotope 0 and its abundance 0 0 1 0 J epsrwts gt For hydrogen component HW If it exchanges with atoms on other molecules type 1 if not type 0 1 epsrwts gt For component HW Type 0 for a natural isotope or mass number for a specific isotope 0 and its abundance 0 0 1 0 J epsrwts gt Type basename of file to output weights to H20 epsrwts gt For total data 1 has data been normalised 1 or not 0 0 epsrwts gt Writing TOTAL weights to file C EPSR examples_rh water making water wt s H20tot wts The key things to note are that 1 epsrwts prompts you for which ato file to use 2 The output is set to be per atom rather than per molecule option 1 3 Weselect only 1 sample 4 epsrwts then goes through each component asking whether it is a natural isotope 0 if it is a natural isotope and 2 if it is deuterium and its abundance and for hydrogen atoms it asks if these can exchange this should be yes 1 if the hydrogen is bonded to oxygen or nitrogen otherwise no 0 5 It asks you for the basename of the
24. e found in this file Component no label atomic fraction chemical symbol 1 0 0 66667E 00 o 2 Si 0 33333E 00 Si epsrwts gt How many samples 1 2 or 3 0 to quit 1 epsrwts gt Get the scattering lengths for all components in the sample epsrwts gt For component O epsrwts gt For component Si epsrwts gt Writing TOTAL weights to file C EPSR examples_rh silica_with_silvia ma king_ato_and_inp sio2tot wts Firstly it asks you to select the ato file to create the wts file for here have typed return until it selects sio2 ato at which point select it by typing y in the usual way We then have to specify if the output is per atom or per molecule select per atom option 1 We tell it that we have just 1 sample even when we have more than one dataset it is best to set up a wts for each dataset individually It then goes through each component found in the ato file asking whether it is a natural isotope or not and their abundances In this example we have only natural isotopes and since we have just one isotope we have abundances of 100 i e 1 0 Finally we have to specify the base name for the wts file we specify sio2 so the weights file is sio2 EPSR wts and whether the total data has been normalized or not in this example it has Making an inp file See section 5 3 So we have set up an initial configuration for our system sio2 ato but before we can run EPSR we have to set up the inp file which controls how EPSR
25. e molecules are identical and their atoms are in exactly the same position To sort this out we spread out the molecules using introtcluster and then give the intramolecular coordinates some disorder to ensure that the molecules are different from each other using fmole Run fmole at least for a 5000 times on water_1000 ato This should leave us with a ato file ready to run looking at it using plotato should give something like this z Al Setting up the weights files Next we have to make a weights file for each dataset we have using the epsrwts command In this example we have three datasets H20 D20 and HDO So we run epsrwts for each of these In fact epsrwts does not ask for the dataset names it only prompts for the ato file name Below is a print out of how to set up the wts file for the nonsubstituted dataset H2O mdcs01 EPSRshell gt epsrwts Filename water_1000 ato Type y to accept u to go back e to exit Y minitc gt Following molecule types found 1 OW 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 1 OW water_temp 0 10000E 01 0 10000E 01 26 891474 31 0516 16 no of molecules to read 1000 3000 3000 2 0 310516E 02 29940 01 0 10020037 Atomic fraction 1 0 33333E 00 Atomic fraction 2 0 66667E 00 no of molecules to read 1000 3000 2 3 epsrwts gt Program to calculate inter and intra molecular weightings for DCS 1st or 2nd order difference data epsrwts gt Is the output to
26. e of plot max 25 1 0 0 0 00100 sphere radius r theta phi r g b colour indices 0 5 0 98 Dr tf Lt 1 sphere radius r theta phi r g b colour indices Then are many options that allow to choose the graphic rendering of the figure They are already set to default values but you can play with them if you wish so EPSRshell gt plot3d 1 shcoeffs lt undefined gt 2 ncoeffs 3 ident 4 setone 1 5 nsmoo 4 6 radmax 5 7 nplotxy b 1 48 8 aspect 1 0 9 rmin_rmax 2 0 5 0 10 surfra 0 15 11 use_11_12 10 12 use nl n2 10 13 use_m 0 14 nvary 1 15 ph th cb 000 16 nsphere 1 17 radsphere 1 0 18 rthetaphi 0 000 19 rgbsph Ont Oar 07 20 axespar p 2 2 21 plottitle 22 titlecoord 0 1 1 3 2 23 blank 24 rgbbak 0 8 0 8 1 0 25 ishade 26 rgbobj 110 27 lightcoord 2 2 0 28 fadefc 0 29 itrans 0 30 appearance 1 0 0 0 1 0 1 0 31 rotelev I5 35 32 extraline 0 33 extratext 0 34 extcoeff SHARM h01 setup input file gt File class plot3d file extension plot3d txt Filename met_oh plot3d txt Type y to accept u to go back e to exit you launch the plot Y A pgplot gif file is output Now vary minimum and maximum radius to plot and the fraction of molecules you want to plot until you manage to understand first and to render the feature that you are interested in highlighting AsO Sad minimum and maximum radius of plot Oss fractional isosurface level ve for absolute 49
27. e type temp changeato then tells us the system s current temperature 1 000K and we change it to 10 000K by typing 10000 We confirm this selection by hitting return and then exit changeato by typing e We also have to tell changeato to save the data to an ato file here have overwritten the original one Now are ready to try and equilibrate our system We can run EPSR once by simply typing epsr at the in the EPSRshell prompt it then asks us for the inp file name This is a good test that all files are present and correct 11 Assuming that you have corrected any problems with running EPSR we now want to run it more than once to do this we create a run script called runscript txt see section 3 4 simple runscript epsr sio2 Then we run it by typing ss runscript txt into EPSRshell EPSR will then run in the bat window that you started the script but you will be unable to interact with and EPSR is running indefinitely To interact with the running EPSR program you have to start a new EPSRshell prompt this can be done also by double clicking on the EPSR bat file in your run directory This brings up a new EPSRshell which informs you that it detects that EPSR is already running we can now either end the script by typing es or pause the script by typing ps and resuming it later by typing ss There is a full description of EPSR s running states and script operation in section 3 4 of the manual Examining the
28. empt EPSRshell gt setup plot3d 1 shcoeffs lt undefined gt 2 ncoeffs 3 ident 4 setone b 5 nsmoo 4 6 radmax 5 7 nplotxy P ee i 8 aspect 1 0 9 rmin_rmax 2 0 5 0 10 surfra 0 15 11 use_11_12 1 0 45 12 use nl n2 1 0 13 use_m 0 14 nvary 4 15 ph th ch 000 16 nsphere 1 17 radsphere 1 0 18 rthetaphi 0 000 19 rgbsph 02 7 O27 O27 20 axespar L524 21 plottitle 22 titlecoord 0 1 1 3 2 23 blank 24 rgbbak 0 8 0 8 1 0 25 ishade 1 26 rgbobj LLO 27 lightcoord 2 2 0 28 fadefc 1 0 29 itrans 0 30 appearance 1 0 0 0 1 0 1 0 31 rotelev 15 35 32 extraline 0 33 extratext 0 34 extcoeff SHARM hO1 setup input file gt File class plot3d file extension plot3d txt File Not Found No files of extension plot3d txt found in directory C EPSR17 run met met_12_ sharm No files selected Type the required filename with extension met_oh setup_input_file gt Full filename C EPSR17 run met met_12_sharm met_oh plot3d txt setup _input file gt Problems with specified input file met_oh plot3d txt will use default values setup plot3d gt setup plot3d gt shcoeffs Name of file containing spherical harmonic coefficient shcoeffs lt undefined gt met C EPSR17 run met met_12_sharm met SHARM dat setup plot3d gt shcoeffs Name of file containing spherical harmonic coefficient shcoeffs met SHARM h01 7 setup plot3d gt ncoeffs no of coefficients determined from coefficients file ncoeffs 497 set
29. ensity of the system at this stage just something realistic that will allow you to get a decent sized box e g rho 0 1 3 gives a box of side L N rho 41 3 where N is the number of atoms in your molecule Check the box side in the ato file see below Now go to your EPSRshell prompt and type makemole 21 Filename methanol mol Type y to accept u to go back e to exit y 1 2 3 bond bond bond angle angle angle rot potential potential potential potential temperature vibtemp density ecoredcore w w 44 w o W W w uo A N m 08 3 1 08 4 1 08 5 1 4 6 1 8965269 411 08 3 1 7615492 4 1 7615492 5 2 0309799 411 08 2 1 7615492 4 1 7615492 5 2 0309799 lt 08 2 1 7615492 3 1 7615492 5 2 0309799 5 11 4 6 0 976 2 2 0309799 3 2 0309799 4 2 0309799 2 5 0 976 1 1 8965269 7 g E E g E G F H H w wu M Be w A A u O EE A w EPSRshell gt Makemole outputs and atm file and an ato file The ato file is the actual file containing the molecular coordinates that constitute your 3D model The atm file tells you the numbering that is being assigned to atoms within your molecule that will be used a lot for setting up input files methanol atm file 4 1 2 LSA a DP P Ie 8 IK LO 1E 2 pals 114 115 116 T S 1132 pE 1 1 gt B 2 3 5 S 6 Note that 32 stays for 3 atoms of which the first one is number 2 The numeration then restarts from number 5 Number of dist
30. fac to 1 we set ereq to 4 0 kJ mol which is about 10 of the system energy To improve the fit it is worth trying to increase ereq remembering to reset the empirical potential by setting ireset to 1 after each change 20 Methanol example The system is pure methanol three samples have been measured on NIMROD a Deuteriated methanol CD30D b Methanol deuteriated on the exchangeable site CH3OD c Methanol deuteriated on the non exchangeable sites CD30H Other information useful to the construction of the simulations are included in the following table g kJ mol o A q e C 0 390 3 700 0 297 M 0 065 1 800 0 000 O 0 585 3 083 0 728 H 0 000 0 000 0 431 density 0 089290015 Making an ato file Take a mol file and modify it to make a methanol molecule such as methanol mol file 4 l L Pa Se Ar Sh e Re e S 1 AL TIZ 247 112 1153 416 11F 113 ILS 1 3M 2 3 O H bond O H 097600 bond C O 1 40000 bond C M 1 08000 angle HOC 104 50000 angle MC M 109 28000 angle MCO 109 28000 potential 0 39000E 00 0 37000E 01 0 12000E 02 0 00000E 00 C potential 0 58500E 00 0 30830E 01 0 16000E 02 0 72800E 00 O potential M 0 65000E 01 0 18000H 01 0 20000E 01 0 00000E 00 H potential H 0 00000E 00 0 00000E 00 0 20000E 01 0 43100E 00 H temperature 0 300000E 03 vibtemp 0 650000E 02 ecoredcore 1 00000 2 GO000 Note that This does not need to be the real d
31. gt introtcluster sio2 ato minitc gt Following molecule types found 10 0 10000E 01 0 10000E 01 2 Si 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 10 6 0 10000E 01 0 10000E 01 2 Si si 0 10000E 01 0 10000E 01 19 431013 22 437 no of molecules to read 750 750 750 2 0 224370E 02 11295 212 0 06639982 Atomic fraction 1 0 66667E 00 Atomic fraction 2 0 33333E 00 no of molecules to read 750 750 2 3 22 437 22 437 0 rotational groups 750 molecules 22 437 22 437 EPSRshell gt And finally we run fmole again once but this time on sio2 ato Visualising our system To view our system we can use the plotato command EPSRshell gt plotats Filename o ato Type y to accept u to go back e to exit Filename si ato Type y to accept u to go back e to exit Filename sio2 ato Type y to accept u to go back e to exit y minitc gt Following molecule types found 10 0 10000E 01 0 10000E 01 2 Si 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 10 0 10000E 01 0 10000E 01 2 Si si 0 10000E 01 0 10000E 01 19 431013 22 437 no of molecules to read 750 750 750 2 0 224370E 02 11295 212 0 06639982 Atomic fraction 1 0 66667E 00 Atomic fraction 2 0 33333E 00 no of molecules to read 750 750 2 3 plotato gt Decide what kind of output you want 1 GNUplot 2 PGplot 3 JMOL plotato gt plotato gt Specify whether to plot all molecules 1 or several centred
32. header contains this information r C C C M C O Cai M M M O M H FO O H H H The total number of functions is given by N N 1 where N is the number of distinct atom types defined in the simulation In this example we have N 4 C M O H For convenience it is a good idea to make a look up table to help you identify which columns correspond to which partial pair correlation function Follow the example below and make sure you enter the atoms in the same order as you have them in your mol file The numbering sequence goes from left to right only numbering distinct pairs e g upper right corner plus diagonal pi hi a en ee a C 1 2 3 4 5 6 7 8 9 10 Now you can plot these functions from the plot routine by typing pt 8 and choosing the block numbers For example by typing b 8 9 10 or b 8 10 and then typing again p this will plot the individual O O O H and H H intermolecular correlations EPSRshell gt plot setup input file gt File class plot file extension plot _defaults txt setup_input_file gt Full filename C EPSR17 run met_11_accumulated plot_default txt setup input file gt Reading input file plot _defaults txt plot gt pe 8 pt 8 Sets the specified plot type plot gt type Type of plot type 8 EPSR site site g r b8 10 find _ ncolumn gt 10 10 find _ncolumn gt 8 21 2 2 2 10 setup_plot_filenames gt There are 10 blocks in the file C EPSR17 run met_11_accu mulated met EPSR g01 setup_blocknu
33. in the same way as we did it before and run EPSR again using the runscript This time looking at the system s energy using the plot p 7 command we can see that the system relaxes further reducing its energy C EPSR examples_rh silica_with_silvia silica_3_mc only_equil_300K sio2 2600 2800 J 3000 l 3200 L J 3400 oo its 3600 F 4 0 100 200 300 400 500 Iteration number And we can see that the fit has improved somewhat 13 C EPSR examples_rh silica_with_silvia silica_3_mc only_equil_300K sio2 1 5 rb J 0 5 S E T Ba F E Pa al At E 7 E N i oot NeutronSiO2s Oi Si L F 1 C Brci f Se eee Se ee at aay F f x 0 5 ZL X 4 Le 1 0 5 10 15 20 Q 1 A Making the fit better prior to refinement We now experiment with the model parameters the van der Waals parameters and the minimum distance parameters These can be changed using the changeato command as we did with the temperature In this case the parameters are pretty good but feel free to experiment Beginning the refinement See section 5 3 in the manual To add the refinement of the empirical potential to the simulation we turn it on by changing some of the parameters in the inp file 1 we set potfac equal to 1 0 and 2 we set the ereq parameter to be 10 or 20 of the energy this is roughly 10 to 20 of the energy we have equilibrated too shown in the p 14 plot in this case we chose 300 kJ
34. inct atom types Number of atoms within the molecules 5 21 08 3 1 08 41 08 5 1 4 6 1 8965269 411 08 3 1 7615492 4 1 7615492 5 2 0309799 1 08 2 1 7615492 4 1 7615492 5 2 0309799 411 08 2 1 7615492 3 1 7615492 5 2 0309799 5 1 1 4 6 0 976 2 20309799 3 2 0309799 4 2 0309799 w N H O R R BRA A m This last numbering is needed for setting up the eventual rotational groups and dihedral angles within the mol file at a later stage it will be useful when setting up the calculation of SDF files methanol mol file 4 ii 2 TAESTE Te E IE ao LE 22 lS ae S aae LES iss ae 1 Cc 3M 2 3 S X H bond O H 0 97600 bond C O 1 40000 23 bond C M 1 08000 angle HOC 104 50000 angle MC M 109 28000 angle MC O 109 28000 potential 0 39000E 00 0 37000E 01 0 12000E 02 0 00000E 00 C potential O 0 58500E 00 0 30830H 01 0 16000E 02 0 72800E 00 O potential M 0 65000E 01 0 18000E 01 0 20000E 01 0 00000E 00 H potential H 0 00000E 00 0 00000E 00 0 20000E 01 0 43100E 00 H temperature 0 300000E 03 vibtemp 0 650000E 02 ecoredcore 1 200000 3 00000 Note that rot 5 1 have defined a rotational group whose axis goes from the Oxygen atom number 5 indicated in the atm file to the Carbon atom number 1 see section 4 3 on command makemole The ato file is now overwritten and it now shows also the rotational groups methanol ato file produced by makemole
35. ing up the weights file We have to run epsrwts once for each of the samples we have measured including once for each of the isotopic compositions We have only one simulation box for a given chemical composition of our sample regardless of how many different isotopic substitution we have performed on it But we need to inform the program about these isotopically substituted samples This is what the weights do For each atom type epsrwts will ask us what the mass number is we use O for natural isotopic composition and the abundance of this atom type 1 if all of it is the same isotopic composition or a fraction number if you have a mixture See also the water example on this For each hydrogen atom we have in our ato file we will be asked whether the hydrogen exchanges with atoms on other molecules This happens only for hydrogen atoms bonded to oxygen and nitrogen atoms This is important because in your real sample a mixture ofCD30D in H O at 1 1 molar fraction say you will have effectively a 1 2 ratio D H in your sample on all of the exchangeable sites in fact you will end up with CD3 0 H D 2 1 in H D 2 1 0 So the weight for those exchangeable sites needs to be calculated accordingly and epsrwts kindly does this for you minitc gt Following molecule types found Le 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 1 C methanol 0 10000E 01 0 10000E 01 35 20844 40 6552 no of molecules to
36. input file gt Run name in input file is different from filename specified C EPSR examples_rh silica_with_silvia silica_2_mc_equil_10000K sio2 ato minitc gt Following molecule types found 10 0 10000E 01 0 10000E 01 2 Si 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 10 o 0 10000E 01 0 10000E 01 2 Si si 0 10000E 01 0 10000E 01 19 431013 22 437 no of molecules to read 750 750 750 2 0 224370E 02 11295 212 0 06639982 Atomic fraction 1 0 66667E 00 Atomic fraction 2 0 33333E 00 no of molecules to read 750 750 2 3 changeato gt There are 2 types of atom in this file Atom type 1 has label O Atom type 2 has label Si changeato gt temp changeato gt temp Temperature of this ato file temp 1000 10000 changeato gt temp Temperature of this ato file temp 10000 2 here T type return 10 changeato gt stepmi Intramolecular translation step stepmi 0 1 7 6 changeato gt Current data have not been saved Type lt CR gt to save or q to exit without saving here I type return changeato gt Current name of file is sio2 ato changeato gt Writing to input file sio2 ato changeato gt File sio2 ato already exists Do you want to overwrite it y or n Y EPSRshell gt Firstly we have the select the ato file we want to alter by cycling through the ato files present in the directory until we get to the one we want which we select by typing y Then to change the temperature w
37. k something like this fnameato water _1000 ato Name of ato file fnamepcof water _1000 pcof Name of potential coefficients file qmin 0 05 Minimum value of Q used for potential fits 0 05 ndata 2 Number of data files to be fit by EPSR data L datafile H20 mdcs01 Name of data file to be fit wtsfile H20tot wts Name of weights file for this data set nrtype 5 Data type see User Manual for more details rshmin 0 7 Minimum radius A used for background subtraction szeros 0 0 Zero limit 0 means use first data point for Q 0 tweak 1 0 Scaling factor for this data set 1 0 efilereq 30 Requested energy amplitude for this data set 1 0 data 2 datafile D20 mdcs01 Name of data file to be fit wtsfile D20tot wts Name of weights file for this data set nrtype 5 Data type see User Manual for more details rshmin 0 7 Minimum radius A used for background subtraction szeros 0 0 Zero limit 0 means use first data point for Q 0 tweak 0 Scaling factor for this data set 1 0 efilereq 0 Requested energy amplitude for this data set 1 0 data 3 datafile HDO mdcs01 Name of data file to be fit wtsfile HDOtot wts Name of weights file for this data set nrtype 5 Data type see User Manual for more details rshmin 0 7 Minimum radius A used for background subtraction szeros 0 0 Zero limit 0 means use first data point for Q 0 tweak 1 0 Scaling factor for this data set 1 0 efilereq 30 Requested energy amplitude for this data set 1
38. l be at the origin Viewing the water ato file using the plotato command you should see a single water molecule like this ZIM iF 0 5 b 0 Bs 0 5 n O O troa Te 0 5 3 yI o 0 5 a io 05 E So next we create our system of multiple molecules say 1000 of them using mixato EPSRshell gt mixato mixato gt How many ATO files do you want to mix 1 mixato gt Search for ato file 1 Filename water ato Type y to accept u to go back e to exit minitc gt Following molecule types found 1 OW 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 1 OW water 0 10000E 01 0 10000E 01 2 6891475 3 10516 no of molecules to read 1 3 3 2 0 310516E 01 29 94001 0 10020036 Atomic fraction 1 0 33333E 00 Atomic fraction 2 0 66667E 00 15 no of molecules to read 1 3 2 3 2 new atom types in file C EPSR examples rh water_2 water_1 making ato water ato Atom type 1 has label OW Atom type 2 has label HW mixato gt How many of these molecules do you want in the mixture 1000 mixato gt Give atomic number density per A 3 of mixture 0 1002 mixato gt Type name of file to put mixture in water 1000 ate EPSRshell gt The main difference from the silica example is that we only have one ato file to mix Here have told mixato to output the 1000 molecules in a file called water_1000 ato If we looked at water_1000 ato now we would see the same thing as we saw for the water ato This is because all th
39. ll be rotated be careful to get it the right way around try not to rotate the ceiling around the light bulb 1 methanol 0 100000E 01 0 100000E 01 Name of the original mol file at the end of the ato file Now run fmole in order to disentangle your molecule and give it some disorder fmole gt Iteration 998 Intramolecular energy 0 10152E 02 No of moves tried 6 No of moves rejected 5 fmolecl gt Average no of neighbours per atom 4 fmole gt Iteration 999 Intramolecular energy 0 10542E 02 No of moves tried 6 No of moves rejected 5 fmolecl gt Average no of neighbours per atom 4 fmole gt Iteration 1000 Intramolecular energy 0 99766E 01 No of moves tried 6 No of moves rejected 4 Done fmole methanol ato file after running fmole 25 i 0 000E 00 6 0 391L226E 01 0 929E 00 0 300000E 0 1 00E 03 01 0 100E 01 0 LOQE O1 0 000000E 00 0 650B 02 0 000000E 00 0 000000E 00 a C 5 2 O0 108E 01 BO p 25 2 p 5 4 0 108E 01 amp O24 R p 5 6 0 190K 01 M 2 4 1 0 108EF01 3 Gs Re 1 25 2 5 E 2 0 er S 01 5S Y e 8 K Ya FOL M 3 4 1 0 108E 01 2 Os Re C lt T Zn b 4 0 e 0 5 G 55 p 0 203601 M 4 4 1 0 10008E 01 2 Oc AF lt Ou 2 10 1 7 2 6 gt 0 203401 O 5 5 l Gelert 85 6 0 976E 00 2 Ure onto t 3 O 20sTt0u 4 0 203EH 01 A 6 a 5 0 KL 9 251p 1 1908 01 pi ROT
40. mbers gt Number of plotting columns 3 plot gt b Block numbers to plot e g 12 59 6 b 8 10 6 find _ ncolumn gt 10 10 find _ncolumn gt 8 2l 2 2 2 10 setup_plot_filenames gt There are 10 blocks in the file C EPSR17 run met_11_accumulated met EPSR g01 setup_blocknumbers gt Number of plotting columns 3 39 1 0 1 0 nn 22 122810 222916 3 2 2 10 18 1 000000 1 000000 CAEPSR17 run met_11_accumulated met r A Spherical harmonics Among many analysis routines one of the most elaborate is the one that calculates the representation in terms of certain special functions called spherical harmonics of the correlations between the atoms correlations see chapter 7 This sort of information is reconstructed from the simulation box and averaged over many configurations of the molecules in the box and it s a useful 3 dimensional view of the information at least in part already contained within the partial pair correlation functions The best way to learn how to use them is to see some examples some are in the manual and we have added one here for the methanol example and start thinking about your own molecule The calculation is performed in two steps 1 Calculation of the spherical harmonics coefficients accumulating over several configurations 2 Representation of the Function obtained The initial calculation doesn t require much thinking about what you want to do just how accurate you ma
41. mol Water example We have 3 diffraction data sets in this example are H2O mdcs01 this undeuteriated pure water D20 mdcs01 this is heavy water and HDO mdcsO1 and this is a 50 50 molar mixture of deuteriated and undeuteriated water Making an ato file We shall construct our system using makemole like we did with silica but this time we just have one mol file since we have just one molecule type Section 4 3 in the manual explains the makemole command and uses water as its first example The process is very similar for what we did in the silica example The water mol file should look like 4 Oo li TS PS 14 IS pe I7 Ps 19 PLO 11 12 13 14 Ls 16 1 Ow 2 3 HW HW bond OW HW 0 97600 angle HW OW HW 104 50000 14 potential OW 0 65000E 00 0 31660E 01 0 16000E 02 0 84760E 00 O potential HW 0 00000E 00 0 00000E 00 0 20000E 01 0 42380E 00 H temperature 0 300000E 03 vibtemp 0 650000E 02 density 0 100200E 00 ecoredcore 1 00000 3 00000 This mol file specifies the water molecule to have O H bonds of length 0 976 and an H O H angle of 104 5 degrees It gives the oxygen atoms sigma values of 3 166 Angstrom and epsilon values of 0 65 kJ mol The hydrogen atoms sigma and epsilon are both zero We run makemole on the water mol file which will create water atm and the water ato files Next we give the atoms in the water ato file some coordinates running fmole at least 9000 times without doing this all the atoms wil
42. newsim C 12 05 2009 21 20 lt DIR gt 12 05 2009 21 20 lt DIR gt 17 04 2009 16 47 168 epsr bat 17 04 2009 16 47 140 epsr sh 17 04 2009 16 47 42 694 0 WaasKirf dat 17 04 2009 16 47 849 gnuatoms txt 17 04 2009 16 47 918 gnubonds txt 17 04 2009 16 47 58 830 plot defaults txt 17 04 2009 16 47 26 runepsr txt 17 04 2009 16 47 64 runepsrbenz txt 17 04 2009 16 47 355 system_commands txt 17 04 2009 16 47 355 system_commands_linux txt 17 04 2009 16 47 469 system_commands windows txt 11 File s 104 868 bytes 2 Dir s 12 104 372 224 bytes free EPSR18 run mynewsim gt Now you can type epsr in order to launch the shell C C G Cc C EPSR18 run mynewsim gt epsr EPSR18 run mynewsim gt set currentdir C EPSR18 run mynewsim EPSR18 run mynewsim gt set EPSRroot C EPSR18 EPSR18 run mynewsim gt set EPSRbin C EPSR18 bin EPSR18 run mynewsim gt cd C EPSR18 bin EPSR18 bin gt call epsrsetup EPSR18 bin gt if defined epsrpath set path EPSR18 bin gt set epsrpath your path EPSR18 bin gt title EPSRsetup EPSR18 bin gt set EPSRroot C EPSR18 EPSR18 bin gt set EPSRbin C EPSR18 bin EPSR18 bin gt set EPSRgnu C EPSR18 bin gnuplot bin EPSR18 bin gt set PGPLOT_DIR C EPSR18 bin PGPLOT PGPLOT1lib EPSR18 bin gt set PGPLOT_FONT C EPSR18 bin PGPLOT PGPLOT LIB grfont dat EPSR18 bin gt set path your path EPSR18 bin gt cd C EPSR18 run mynewsim EPSR18 run mynewsim gt cop
43. nitc gt Following molecule types found 10 0 10000E 01 0 10000E 01 2 Si 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 10 o 0 10000E 01 0 10000E 01 2 Si si 0 10000E 01 0 10000E 01 2 118229 2 44592 no of molecules to read al al p 2 0 244592E 01 14 632776 0 06833973 Atomic fraction 1 0 00000E 00 Atomic fraction 2 0 10000E 01 no of molecules to read i 1 2 3 1 new atom types in file C EPSR examples_ rh silica_with_silvia making_ato_an d_inp 2 si ato Atom type 2 has label Si mixato gt How many of these molecules do you want in the mixture 250 mixato gt Give atomic number density per A 3 of mixture 0 0664 mixato gt Type name of file to put mixture in 8i62 ato EPSRshell gt After running the mixato command it asks you for how many ato files you want to mix in this case we want to mix si ato and o ato It the searches for the ato files in the directory It then asks which ones you want to mix to skip an ato file simply press return and to accept one type y Then for each file you chose it asks how many of these molecules you want in the new ato file Finally it asks for the atomic number density in this example 0 0664 and finally the name of the ato file to write the mixed system out to here chose sio2 ato We can the view file using plotato see manual section 3 7 and we see that all the atoms are overlapping So we run introtcluster on sio2 ato to spread the atoms out EPSRshell
44. older contains some examples of mol files that you can copy and modify finally the run folder is where you are supposed to set up your own simulation In principle you can run your simulation also from other places but not from a folder that contains spaces in the name so avoid My Documents or the Desktop The run folder contains a startupfiles subfolder that contains most of the files that you need in each of your working folders and to which you will just have to add you data and the other files essentially ato inp and wts that you will create by following the instruction given below You should have in particular an EPSR bat file double click to run the batch file right click and choose edit to edit it looking like this set currentdir CD set EPSRroot C EPSR18 set EPSRbin EPSRroot bin cd SEPSRbin call epsrsetup cd Scurrentdir copy system commands windows txt system _commands txt title EPSR in CD ae EPSRbin epsrshell The EPSR bat file calls the EPSRsetup bat file in the bin folder The EPSRsetup bat file looks like this if defined epsrpath set path Sepsrpath set epsrpath spath title EPSRsetup set EPSRroot C EPSR18 set EPSRbin EPSRroot bin set EPSRgnu sEPSRbin gnuplot bin Sec PGPLOT DIR EPSRbin PGPLOT PGPLOT1lib set PGPLOT FONT EPSRbin PGPLOT PGPLOT LIB grfont dat set path sPGPLOT DIR sepsrpath If you want to modify the way EPS
45. or central molecule axiscl z 6 Setup sharm gt axisc2 Second axis definition for central molecule 43 eae dL 2 w L H a Q N Setup sharm gt atom s Second molecule list of centre atom types atom s O Setup sharm gt axiss2 Second axis definition for second molecule axiss2 x 1 Setup sharm gt Current data have not been saved Setup sharm gt Current name of file is met SHARM dat Setup sharm gt Writing to input file met SHARM dat EPSRshell gt met SHARM dat met SHARM Title of this file fnameato met ato Name of ato file ny 10 Number of radius values max 200 rmax 10 Maximum radius for spherical harmonic coefficients nsumt 0 Number of configurations already accumulated ncoeffs 0 Number of coefficients program calculates q Once the coefficients are calculated we can decide what type of information exactly we want to extract This requires a little thinking since setting certain indexes to the coefficients to zero is equivalent to integrating along certain spatial angular variables For simplification purposes it is possible to divide the number of possible function may want to inspect in two categories 1 where molecule 2 sits with respect to molecule 1 Spatial Density Function or SDF 2 what is their relative orientations Orientational correlation Function or OCF Spatial Density Function is the easier to set up and understand by selecting as in the example below 44
46. read 1000 6000 6000 4 0 406552E 02 67196 76 0 089290015 Atomic fraction 1 0 16667E 00 0 50000E 00 Atomic fraction 0 16667E 00 2 Atomic fraction 3 Atomic fraction 4 0 16667E 00 no of molecules to read 1000 6000 4 10 epsrwts gt Program to calculate inter and intra molecular weightings for DCS 1st or 2nd order difference data epsrwts gt Is the output to be per atom 1 or per molecule 2 1 epsrwts gt The following components were found in this file Component no label atomic fraction chemical symbol t Cc 0 16667E 00 C 2 M 0 50000E 00 H 3 6 0 16667E 00 0 4 H 0 16667E 00 H epsrwts gt How many samples 1 2 or 3 0 to quit 1 epsrwts gt Get the scattering lengths for all components in the sample 34 LD 3 3 GU S a GU CL DU S oO eb gt oO wn oO Q Cc oO S O oO LS Zu w wn oO gt wn O 5 e wn oO x DU 3 R CD30D CD30H CH30D exch mass exch mass exch mass C 0 1 0 1 0 1 M 0 2 1 0 2 1 0 0 1 0 0 1 0 1 0 1 H 1 2 1 1 0 1 1 2 1 Note that epsrwts gt Type basename of file to output weights to cd30d_ The output file will be called cd30d_tot wts epsrwts gt For total data 1 has data been normalised 1 or not 0 0 Files output by Gudrun mdcs01 are not normalised e g divided by the total cross section of the sample Making an inp file Now we first make setup epsr write
47. type nrtype is 3 it is a Genie II histogram format So summarising our inputs to the simulation 1 The ato file contain the molecular geometry the sample composition and the density of the system moreover it contains the parameters for the reference potential 2 The wts files contain the diffraction data description remember to put also the diffraction data in the folder 3 The inp file contains the names of all these indispensable files and the flags we need in order to run the program Running EPSR Equilibration at 10 000K First off we just want to run a MC simulation without any refinement so we have to make sure that the potfac parameter in the inp is set to 0 This means that we are running without the empirical potential being calculated To speed up the equilibration of the system we want to run at 10000K To change the temperature that we are running at we have to change the ato file by using the changeato command EPSRshell gt Ghang ato setup input file gt File class changeato file extension ato Filename o ato Type y to accept u to go back e to exit here I type return Filename si ato Type y to accept u to go back e to exit There I type return Filename sio2 ato Type y to accept u to go back e to exit y setup_input_ file gt Full filename C EPSR examples_rh silica_with_silvia silica_ 2_mc_equil_10000K sio2 ato setup_input_ file gt Reading input file sio2 ato setup
48. up plot3d gt ident 0 for identical molecules else 1 if different ident 0 e setup plot3d gt Current data have not been saved Type lt CR gt to save or q to exit without saving 46 setup plot3d gt Current name of file is met_oh plot3d txt setup plot3d gt Writing to input file met_oh plot3d txt EPSRshell gt Note You have to type the root e g met for the SHARM h01 file then you scroll through the options and you ll see that EPSR is able to retrieve the number of coefficients from this file At this point it s probably easier to exit the dialogue window and modify the file from the editor met_oh plot3d txt met SHARM hO1 497 no of coefficients determined from coefficients file 0 for identical molecules else 1 if different 0 sets first coefficient to zero normally 1 number of smoothings on coefficients KA no of plots along x and y axis set at 1 1 1 1 aspect ratio of plot 1 9 Ea i 3 1 5 2 1 axes character size line width and colour separated by spaces 0 1 1 3 2 x y coords of title and character size separated by spaces 0 8 0 8 1 0 red green blue fractions for background separated by spaces i ishade 1 8 0 means no shading ve means inverted shading p E s red green blue fractions for object separated by spaces 2 2 0 x y z coordinates for light source separated by spaces 1 0 fade factor 0 no fading 1 full fading 0
49. we have to type 0 0 0 0 0 to specify no bonds The final two responses we have to give to plotato specify how we want GNUplot to plot the system here have just kept the atoms at the default size and given a plot rotation of 30 30 Once the plot has appeared we can change the rotation using the mouse Provided the ato file has been created correctly we should have something which looks like the plot below 10 ox v IA Setting up the weights file See section 5 1 Next up we have to set up the weights file wts file This is done using the epsrwts command EPSRshell gt Spsrwts Filename o ato Type y to accept u to go back e to exit here IT type return Filename si ato Type y to accept u to go back e to exit There I type return Filename sio2 ato Type y to accept u to go back e to exit y minitc gt Following molecule types found 10 0 10000E 01 0 10000E 01 2 Si 0 10000E 01 0 10000E 01 minitc gt Following molecule types found 10 0 0 10000E 01 0 10000E 01 2 Si si 0 10000E 01 0 10000E 01 19 431013 22 437 no of molecules to read 750 750 750 2 0 224370E 02 11295 212 0 06639982 Atomic fraction 1 0 66667E 00 Atomic fraction 2 0 33333E 00 no of molecules to read 750 750 2 3 epsrwts gt Program to calculate inter and intra molecular weightings for DCS 1st or 2nd order difference data epsrwts gt Is the output to be per atom 1 or per molecule 2 1 epsrwts gt The following components wer
50. y system_commands windows txt system_commands txt 1 file s copied EPSR18 run mynewsim gt title EPSR in C EPSR18 run mynewsim EPSR18 run mynewsim gt C EPSR18 bin epsrshell EPSRshell gt Welcome to EPSR version 18 2009 04 01 Type help or for a list of commands Binaries folder EPSRbin Home folder is C EPSR18 run mynewsim EPSRshel1 gt You can see that the prompt is now EPSRShell gt Amorphous silica example The chemical formula for silica is SiO So in our system we have two oxygen atoms for every silicon atom This is an interesting example as it is possible to get a quite good fit to the experimental data without potential refinement so we shall try this before bringing in the empirical potential In order to speed up the initial equilibration of the system it is a good idea to run it at a high temperature for example 400K and then equilibrate to the desired temperature in this case 300K There is only one set of neutron data used in this example NeutronSiO2sq dat and this has been normalized The parameters for the reference potential are given in the table below Silicon Oxygen Epsilon kimol 14 os o6 Sigma 1 03 3 11 Mass amu 28 16 Charge e 2 1 Atomic number density atoms 3 0 06634 Making an ato file See section 4 1 in the manual Our first task is to make the file containing the system the ato file in this case this would consist of say 250 silicon atoms and 500 oxygen
51. y want you calculation to be e g where to truncate your expansion A typical starting value is given in the example below as We consider two molecules one at the centre with a specific orientation and we go and look at the position of orientation of another molecule of the same type or of a different type with respect to this first one You need to have some basic knowledge about the geometry of your molecule because the presence of symmetries simplifies the calculation Here it is required to provide the category of a rotational symmetry axis of the molecule according to molecular point group symmetry A symmetry axis is an axis around which a rotation by 360 n results in a molecule indistinguishable from the original This is also called an n fold rotational axis and abbreviated Cn Examples are the C2 in water and the C3 in ammonia A molecule can have more than one symmetry axis the one with the highest n is called the principal axis and by convention is assigned the z axis in a Cartesian coordinate system If the molecule has cylindrical symmetry e g an OH ion nis 0 and 1 if the molecule doesn t have any rotational symmetry axis then it belongs to C1 Then we have to define a frame reference attached to each of the two molecules bearing in mind 41 Quoting from the manual For the first axis z in this example the specified axis is assumed to run from the centre of the molecule to the mid point of the specified atoms
52. ype see User Manual for more details rshmin 0 7 Minimum radius A used for background subtraction szeros 0 0 Zero limit 0 means use first data point for Q 0 tweak L0 Scaling factor for this data set 1 0 efileregq 150 Requested energy amplitude for this data set 1 0 q Note nrtype 5 Data type see User Manual for more details This is the correct filetype for files output by Gudrun Running EPSR Now we check first of all if the program will run by typing epsr met where met is the name of your inp file The first time you do this it doesn t find the met pcof file but it doesn t matter because it will create it Afterwards you can create a script to run EPSR multiple times Now continue to equilibrating refining and accumulating as explained in the previous examples 37 Examining the results When visualising your results it may be useful to know the meaning of all the extension of the numerous files output by EPSR listed in the table below In this way you can also use you preferred program other than the plot routine to look at your results SIM DATA DIFF SIM DATA POT COORD Totals U01 01 VO1 X01 WO1 mdcs mgor Partials FO1 Q01 DO1 GO1 ROL PO1 Z01 Intramol Partials SO1 YO1 Intermol 38 Visualising your partials The partial pair correlation functions or partials are written in the met EPSR g01 file asa sequence of columns of the form r partial1 error partial2 error The

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