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RMCProfile User Manual

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1. 2 2 CocsPeALKENE 2 gt SO2SULFONE Cosp2aLkKENE Ccsp2ALKENE SISILANE Cosp2aLkKENE Ccsp2aLKENE CCYCLOPROPANE CocsPeaL kENE CcsPoaLkENE P gt gt gt Cosp2aLkeENE Ccsp2aLKENE GEGERMANIUM 120 Ccsp2aLkene Ccsp2aLkene NysP2PYRROLE Cosp2aLkeENE Ccsp2aLKENE Oosp2FURAN CosPeALKENE CCSP2ALKENE SSSP2THIOPHENE Cosp2aLkKENE Ccs P2ALKENE N NOAZOXY LOCAL Cosp2aLkENE Ccsp2aLkKENE NNitRO Cosp2aLkKENE Ccsp2aLKENE Ccsp2cYCLOBUTENE CocsPeaLkENE CcsPoaLkENE N NOHOXIME CocsPeaLkENE CcsP2ALKENE NN PYRIDINIUM NN AZOXY DELOC LKENE HEXCEPTONN O S LKENE NNsp2PYRROLE 5 LKENE HEXCEPTONN O S 0 LKENE Nnsp3 LKENE NNsP2 LKENE F FLUORIDE LKENE CIcHLORIDE LKENE liopIDE LKENE S gt SO2SULFONE LKENESISILANE LKENE CcYCLOPROPANE LKENE G GERMANIUM 2 2 BOND BENDING TERMS 122 00
2. 0 5 Nuspa CcsPsaLkANE CYCLOPROPANE 2 2 BOND BENDING TERMS 105 000 106 000 109 500 109 410 111 000 109 939 110 000 111 000 112 000 109 500 110 500 110 500 107 600 107 500 104 700 109 400 110 000 107 500 109 000 109 500 110 100 109 500 101 000 109 000 108 500 105 500 104 500 106 500 107 000 109 380 109 600 108 700 103 100 108 500 107 500 107 000 104 100 110 740 109 500 8 926 8 613 6 741 7 365 7 115 6 217 7 240 5 243 4 369 1 248 4 119 4 119 6 866 10 024 11 235 4 494 11 485 9 987 9 487 6 866 7 365 6 117 12 608 7 365 10 424 11 235 11 859 11 547 11 235 10 611 6 491 11 485 6 741 8 364 10 361 8 738 14 980 13 045 7 490 130 154 Manual v6 5 2 2 2 BOND BENDING TERMS NwsPa CcsPaaLKANE NNSPSAMMONIUM 110 740 13 045 NwsP2 csP3ALKANE SS SULFIDE 107 000 7 240 2 111 000 9 487 5 106 100 24 342 110 400 9 362 109 400 8 988 108 100 9 487 110 700 8
3. gt 107 500 7 490 gt BTRIGONAL 110 920 4 731 C RADICAL 110 000 5 617 CcsesaLkaNE CcsPsaLkaNE GeGERMANIUM 109 300 5 617 CosPaaLkaNE CcsPsALKANE Sri 110 200 6 991 110 200 3 745 Cosp3aLkaNE CcsP3ALKANE S SELENIUM 108 200 6 242 108 200 6 242 110 100 7 365 PYR DELOCLZD 110 740 6 242 103 500 6 778 2 107 500 11 235 Cosp3aLKANE Ccsp3ALKANE N NoAzoxy LOCAL 104 500 5 617 106 000 12 483 Cosp3aLKANE CcsP3ALKANE CBENZENE LOCALIZED 110 600 6 741 109 500 8 364 CcsPaaLkaNE CcsPsaLKANE CcsP2CYCLOBUTENE 110 600 6 741 CosPaaLkaNE CcsPsALKANE OkETONIUMOXYGEN 104 100 13 482 CcsPsALKANE CKETONIUMCARBON 109 000 4 494 CospsaLkaNE CcsPsaLkaNE NN AZOXY LOCAL 108 500 6 242 CosPsaLkaNE CcsPsaLKANENN IMMINIUM 105 000 5 680 Cosp3aLKANE
4. gt 9 gt lt gt TUNTUD 53 gt 2 2 bsty 9 gt 53 2 2 uorsue gt KA3aedoad TUNTUD 53 gt 979 gt 53 lt 21 sdems 132132 2 98 gt 3 lt 9 3 gt 27 154 RMCProfile Manual v6 5 2 CHAPTER 3 INSTALLING AND RUNNING RMCPROFILE Chapter 3 Installing and Running RMCProfile 3 1 Installation We strongly recommend at this point that you put this manual to one side and refer instead to rmcprofile tutorial pdf which will guide you through t
5. 2 124 500 4 494 8 112 500 0 624 3 113 000 5 368 8 113 000 4 494 8 117 400 4 494 SisiLaANe CcvcLoPRoPANE CcvcLoPROPANE 118 000 6 616 CcycLopROPANE C cYCLOPROPANE CCYCLOPROPANE 119 500 4 494 CcycLopROPANE CcYCLOPROPANE GEGERMANIUM 117 000 6 242 CcycLopRopANE CcycLoPROPANE NNitRO 114 600 14 980 Cosp3aLkaNe P gt 95 600 9 612 gt 2 92 500 5 992 0 5 94 700 8 801 CcospzaLkene P gt PPHOSPHINE CCSP2ALKENE 95 000 5 992 HEXCEPTONN O S P gt 92 200 8 489 0 0 gt 0 0 0 99 500 5 617 Ccsp3ALKANE B gt BTRIGONAL OcO H C O C 0 0 122 371 5 692 Ccsp2aLKENE B gt BTRIGONAL Oco H C O C 0 0 126 986 7 540 Oco H c_o c o o B striGoNAL Oco H c 0 c 0 0 119 860 9 113 Ccosp3aLkane C RapicaL CcsP3ALKANE 119 000 6 242 Cosp3aLKane C RapicaL HexcePTONN 0 s 118 000 5 243
6. 107 614 9 163 HexcEPTONN O s S sozsULFONAMIDE NNSP3SULFONAMIDE 100 776 11 410 Oo ccARBONYL S gt so28ULFONAMIDE OO CCARBONYL 122 966 8 239 Oo ccARBONYL S gt SO2SULFONAMIDE NNSP3SULFONAMIDE 107 883 20 747 CcsesaLkaNE NNsP3sULFONAMIDE CCSPSALKANE 111 163 16 178 CcsesaLkaNE NNsP3sULFONAMIDE HNHAMINE IMINE 109 505 7 078 CcsPsaLkaNE NNSP3SULFONAMIDE S gt SO2SULFONAMIDE 109 551 14 855 HNHAMINE IMINE NNsPsSULFONAMIDE HNHAMINE IMINE 109 688 7 590 HNHAMINE IMINE NNsp3sULFONAMIDE S gt SO2SULFONAMIDE 103 248 7 228 gt 118 800 11 235 HoHALCOHOL Oop oPHOSPHATE P gt 112 000 4 744 Table 4 Bond bending terms from the protein set parameters deg Ke eV Catkane Csp3 C Alkane Csp3 C Alkane Csp3 109 500 8 364 Catkane Csp3 C alkane Csp3 C amide 110 600 9 987 Catkane Csp3 C Alkane Csp3 C Carboxyl 110 600 9 987 CAlkane Csp3 C Alkane Csp3 C Phenyl 110 600 6 741 Catkane Csp3 C alkane Csp3 C Alkene His TrpC C 110 600 6 741 Catkane Csp3 C alkane Csp3 Namide 109 480 9 362 Catkane Csp3 C alkane Csp3 Nammonium 103 500 7 115 CaAlkane Csp3 C Alkane Csp3 NGuanidinium 109 480 9 362 CAlkane Csp3 C Alkane Csp3 C Alcohol Phenol 107 500 10 361 Catkane Csp3 C Alkane Csp3 9Sulfide 108 000 9 238 Alka
7. CcsP2ALKENE 107 000 4 993 Ccospeatkene Nnsp2 Ccsp2carBONYL 115 000 7 490 2 110 000 6 242 CcspecarsonyL Nnsp2 Ccsp2carBONyL 124 000 11 235 CcspacarsonyL Nnsp2 HyNn c oAMiDE 118 500 7 240 S gt 122 000 3 745 2 123 000 5 118 120 500 7 240 Hyn c oamip e Nnsp2 CcspscycLoBuTANE 118 300 14 356 Hyn c oamipe Nwsp2 Cc ocycLoBUTANONE 119 200 12 483 CcspaaLKANE Ss SULFIDE CCSP3ALKANE 95 900 10 486 CcspaaLKANE Ss SULFIDE SS SULFIDE 101 800 12 483 CcspsaLKANE Ss suLFipbeE HsHTHIOL 96 000 8 114 Ss suLFipe Ss sutribE HsHTHioL 92 200 9 650 9 92 900 9 113 CcsPsaLkaNE S s sULFONIUM CCSPSALKANE 94 300 6 242 9 gt S SULFONIUMHEXCEPTONN O S 94 000 4 993 9 gt s osULFOxiDE CCsPSALKANE 94 400 14 980 CospsaLKANE 9 gt OSULFOXIDE HEXxCEPTONN O S 90 000 10 736 9 gt S OSULFOXIDE O0 CCARBONYL 105 600 9 987 HeXCEPTONN O S S gt S OSULFOXIDE O0 CCARBONYL 109 600 10 736 136 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS gt SO2SULFONE C CSP3ALKANE 101 600 10 611 9 gt
8. 109 500 8 364 HexcEPTONN O S SisiLane SisiLane 109 400 4 369 HexcEPTONN O S SisiLane CcyCLOPROPANE 110 200 5 742 HexcEPTONN O S SisiLane CcspscYCLOBUTANE 109 300 5 617 112 000 7 490 SisiLane SisiLane SisiLane 118 000 3 121 CcspacYCLOBUTANE SisiLANE C csp3CYCLOBUTANE 124 500 5 992 120 000 8 364 CospsaLkKANE CcycLOPROPANE HEXCEPTONN O S 117 100 7 490 CcspaaLKANE CcYCLOPROPANECCYCLOPROPANE 112 000 7 490 115 000 6 991 Cosp2aLkENe CcycLoPROPANE CCSP2ALKENE 120 000 5 617 5 128 500 4 494 122 000 7 490 115 000 6 991 0 5 123 500 4 494 137 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS 5 0 5 116 500 3 121 5 124 500 2 996 HexcEPTONN O S CcyCLOPROPANE CCYCLOPROPANE 116 800 8 114 HexcEPTONN O S CcyCLOPROPANE G GERMANIUM 119 000 4 993 3
9. 4 4 2 The spin configuration file The starting spin configuration is contained within one file with the name MAGNETISM FILE STEM cfg This has a fairly simple structure much like the classic version 3 files An example is shown below 0 095105 576 2 192 384 0 00000000 0 00000000 1 00000000 0 00000000 0 00000000 1 00000000 0 00000000 0 00000000 1 00000000 The first line contains the atomic number density of the system here 0 095105 the total number of magnetic atoms and hence the number of entries in this file 576 and the number of different magnetic atom types 2 The following line contains the number of atoms of each type present These should be listed in the correct order and should sum to give the total number of magnetic atoms here 192 384 576 There then follows a list of all the magnetic spin vectors in the structure These are unit vectors and should correspond to the atom positions listed in the main configuration file the nth vector listed in the compound_spin cfg file should correspond to the atom whose coordinates are listed the nth entry in the main compound cfg compound rmc6f file The generation rate of standard translational moves is unspecified and will take up the remaining fraction once magnetic and swap moves have been accounted for Common sense will tell you that the total fraction of generated moves specified by the user spin swap should not exceed
10. 0 5 5 5 5 5 3 HexcePrONN o s CcsPsA 0 5 0 5 0 5 5 LKANE S gt S OSULFOXIDE LKANE S gt SO2SULFONE LKANE SISILANE LKANE CCYCLOPROPANE LKANE P PPHOSPHINE LKANE B gt BTRIGONAL LKANE C RADICAL LKANE G GERMANIUM LKANE SNTIN LKANE PDLEapitv LKANES SELENIUM TETELLURIUM LKANE DpEurERIUM LKANE NN c PYR DELOCLZD LKANE NNSPSAMMONIUM LKANE NNsP2PYRROLE LKANE OosP2FURAN LKANE N NOAZOXY LOCAL LKANE NNiTRO LKANE CBENZENE LOCALIZED LKANE CCSP3CYCLOBUTANE LKANE C CSP2CYCLOBUTENE LKANE OKETONIUMOXYGEN LKANE CKETONIUMCARBON LKANE NN AZOXY LOCAL LKANE NN IMMINIUM LKANE NN PYRIDINIUM NOHHYDROXYAMINE LKANE N gt NOHHYDROXYAMINE LKANE NNSP3HYDRAZINE LKANE P gt 0 0 0
11. 1 26 5 323 Ccsp2atkene Nnsp2pYRROLE 1 27 5 323 1 22 5 855 CcsPezALKENE SSsP2THIOPHENE 1 54 3 442 Cosp2aLkene N noazoxy Local 121 1 920 1 47 2 424 CosPeaLkENE CBENZENE LOCALIZED 1 43 2 584 CcsPeaLkENE CcsPscYCLOBUTANE 1 50 3 024 Cosp2aLkENE CcsP2cYCLOBUTENE 1 33 3 600 122 154 RMCProfile Manual v6 5 2 2 1 BOND STRETCHING TERMS CosPeALKkENE N NIMINE LOCALZD 1 27 4 319 2 131 5 711 1 28 4 176 CosP2ALKENE NN IMMINIUM 1 28 4 799 CocsP2ALKENE NN PYRIDINIUM 1 27 3 984 CcsreaLkENE N NOAXOXY DELOC 0 83 1 824 CocsPoaLKENE NN AZOXY DELOC 1 40 2 496 CcsrecanBoNvL CCsP2CARBONYL 1 22 5 399 CcsPecanBONYL HEXCEPTONN O S 1 12 2 097 0 0 0 1 35 2 880 Ccsp2carBonyL Oo ccARBONYL 1 21 4 847 CcspacarsonyL Nnsp2 1 88 3 216 Ccsp2carsonyL F FLUORIDE 1 38 2 016 CcspacarBonyL ClcHLorIDE 1 82 1 382 1 99 1 344 liopipE 2 23 1 248 Ccsp2carBonyL CcYCLOPROPANE 145 2 112 CcspecarsonyL DpeuTERIUM 111 2 097 Ccsp2caRBONYL OCARBOXYLATEION 1 28 3 376 CcspecarBonyL Ccsp3cYCLOBUTANE 1 51 2 304 CcspecarBonyL Ccsp2cyCLOBUTENE 1 35 4 607 Ccsp2caRBONYL OOH O C CARBOXYL 1 35 2 880 1 21 5 18
12. 120 000 5 617 2 2 120 000 6 242 CcspsaLkaNE CcsP2ALKENE S SSP2THIOPHENE 120 000 8 738 5 20 123 000 8 988 117 400 5 867 117 830 10 860 CcsreaLkENE CcsPeALKENE CCSP2ALKENE 122 000 9 487 gt 115 500 6 242 5 120 000 6 117 0 121 900 7 490 131 154 RMCProfile Manual v6 5 2 CospecarBonyL Cesp2a CocsPecanBoNvL CcsP2A 5 2 0 5 0 5 0 5 0 5 0 5 0 5 HeXCEPTONN O S CcsP2a HeXcCEPTONN O S CcsP2a HeXcCEPTONN O S CcsP2a HeXcCEPTONN O S CcsP2a HexcEPTONN O S Ccsp2a 132 154 5 5 2 FLUORIDE
13. 3 3 117 000 5 243 2 6 2 120 000 4 993 109 500 6 242 2 110 900 6 242 Cosp3aLkKANE G GERMANIUM HeExcEPTONN O S 110 200 4 868 CcspaaLKANe G GERMANIUM GEGERMANIUM 111 500 4 369 109 500 6 242 CosPeaLkENE GeaERMANIUM HEXCEPTONN O S 110 100 4 868 Ccsp2atkene GEGeRMANIUM GEGERMANIUM 109 500 6 242 3 107 500 5 280 5 108 800 4 993 5 114 500 4 369 5 105 200 6 366 112 500 3 745 CocsPsaLkaNE Sh riN CcsP3ALKANE 107 000 3 995 138 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS CospsaLkaANE SNTiIN HeExcEPTONN O S 110 500 2 834 8 S riN HEXCEPTONN O S 109 500 1 648 CcspaALkaNE P Di gap v CcsP3ALKANE 109 500 1 248 5 109 500 1 248 109 500
14. 2 5 gt so2sULFONE 1 66 2 928 1 03 3 249 NNsP2 CCARBONIUMION 1 32 3 278 55 5 1 1 5 5 1 2 02 1 257 Ss 1 34 1 857 SisiLane SisiLane 2 32 0 792 SisiLane CcYCLOPROPANE 1 84 1 680 Sisitane CcspscycLOBUTANE 1 88 0 624 HoHaLcoHoL O gt NOHHYDROXYAMINE 0 97 3 600 0 95 3 734 CcycLopRoPANE CcYCLOPROPANE 1 49 2 400 CcycLopROPANE G GERMANIUM 1 91 1 296 CovcLoPRoPANE CcsPecvcLoPROPENE 1 49 2 112 CcycLopropane Nwitro 1 48 2 088 CcvcLoPRoPANE CcsPscvcLOBUTANE 1 50 2 112 HNHAMINE IMINE Nn c PYR DELOCLZD 103 2 736 1 03 3 120 2 1 04 2 649 20 1 02 2 865 HNHAMINE IMINE NN N AZO LOCAL 1 03 2 568 HNHAMINE IMINE NN azoxy LOCAL 1 03 2 856 1 02 3 129 101 3 129 HNHAMINE IMINE N gt NOHHYDROXYAMINE 1 02 2 952 HNHAMINE IMINE NNsp3HYDRAZINE 1 02 3 052 HNHAMINE IMINE NNsp3SULFONAMIDE 1 02 3 061 0 97 3 432 Ge GERMANIUM 2 40 0 696 Pbigap vy Pbigap v 1 94 0 984 Nu c PvR pELocLzbj NN c PYR pELocuzp 1 25 4 559 Nu c PvR DELOCLZD NNsP2PYRROLE 123 5 279
15. 37 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE POTENTIALS 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 58 PRESSURE 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 R SPACING Requires the value of the spacing used in the pair distribution functions Currently the units are not interpreted default units are Angstroms RMC NOTE 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 SAVE CONFIGURATION FORMAT 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 SAVE PERIOD Requires time period in minutes between sav ing the configuration SORT ATOMS Gives a flag to sort the atoms in in the input con figuration for version 6 configuration files into the order of atom type Is useful when the g
16. 5 0 110 000 10 236 5 109 300 10 236 3 5 2 111 000 9 487 0 8 108 500 8 988 5 105 660 9 362 5 106 500 6 366 HexcEPTONN O S CcsP3ALKANE lioDIDE 102 800 7 740 HexcEPTONN O S CcsP3ALKANE SS SULFIDE 110 800 9 238 3 gt 5 SULFONIUM 108 200 3 745 RMCProfile Manual v6 5 2 0 8 0 8 0 8 0 8 0 5 0 5 0 5 0 5 0 5 0 5 0 8 HeXCEPTONN O S CcsP3a HexcePrTONN o s CcsPsA HeXcCEPTONN O S CcsP3a HeXCEPTONN O S CcsP3a HeXCEPTONN O S CcsP3a 0 5 0 5 0 5 0 5 0 5
17. is a keyword that denotes the property to be extracted The keywords are defined as XPath expressions in the file called zmcprofile config which in the example command is found 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 110 154 RMCProfile Manual v6 5 2 6 3 CML BASED ANALYSIS TOOLS Table 6 1 Default list of summon keywords for RMCProfile output XML files Keyword atoms Bragg_background Bragg_profile_type Bragg_weighting close_approach Comment DataNote diff Bragg diff PDF1 diff_QiQl dSpacing exp Bragg _ 1 0101 hkl recalculate Investigator Keywords lattice vectors maximum distances maximum moves minimum distances neutron coeffs PDF1 5 501 nnpdf nnsq number avcoord constraints number coord constraints number density number of species numbers of species nxsq offset flag offsets partiall Phase Pressure print period Q 0101 renorm_flag RMC_Bragg 0101 RMCNote save_period supercell Temperature time_limit weights Description of data List of atom types Coefficients for background function in Bragg profile Bragg profile function used Weight applied to Bragg profile fitting Closest approaches allowed in simulation Metadata comment Metadata note about data
18. 2 2 Bond bending terms Table Bond bending terms from the standard data set deg eV CosPaaLkaNE CcsPsALKANE CCSPSALKANE 109 500 8 364 CcspsaLkaNE CcsPsaLKANE CCSP2ALKENE 110 600 6 741 CCSP2CARBONYL 110 600 9 987 108 800 11 984 5 109 800 7 365 107 500 10 361 109 470 9 737 Cosp3aLkane CcspsaLKANe Nnsp2 109 480 9 362 Cosp3aLkaNE CcsPsALKANE F FLUORIDE 107 300 11 485 Cosp3aLkaNe CcsPsALKANE ClIcHLoRIDE 106 200 9 987 5 108 200 9 238 106 000 8 114 127 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS Cosp3aLkaNE CcsPsALKANE SS SULFIDE 108 000 9 238 Cosp3aLkaNE CcsPsALKANE S gt S SULFONIUM 107 800 5 243 9 gt S OSULFOXIDE 107 500 8 114 gt 80250 103 000 10 860 915 109 000 4 993 114 400 4 369
19. gt 1 1 1 4 3 5 Implementation within RMCProfile 4 3 USING EXPERIMENTAL DATA gt 0 4 20 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 Function Input text in Keen Eqn here Limiting values 1 0 25 4 6 Lj Gb 0 F Q 0 11 4 6 Lj ob 0 S Q 540 4 9 ob Lj jb Lj 1 0 Xj ob Q 0 QF Q XjgbjQ 0 i Q normalised 4 19 120 normalised 4 19 120 5 0 normalised 19 4 19 1 Xj cb gt 1 G r G r 10 4 2 4 7 gt 0 x 4 4 0 gt E D r 26 4 11 0 T 27 412 0 4 cjbj r Gnom r G r normalised 415 ed Grom r x normalised 16 4 15 0 1 Dnorm r D r normalised 4 16 0 T r normalised 4 16 0 7 5 spelling normalized works just as well 55 154 RMCProfile Manual
20. gt END POINT End point of the data an integer FILENAME Filename containing the data gt FIT_TYPE Gives the function that is fitted options are T r D r Or together with the word normalised Or normalized for functions that are scaled by the neutron scattering coefficient c cjbibj to give limiting values of 1 depending on the func tion This is explained in more detail in section 4 3 5 FITTED OFFSET If specified this instructs the program to fit the offset value provided for this set of data Default is not to fit GUDRUN If specified the data file was generated by the Gu drun data reduction suite and contains errors on each point NEUTRON COEFFICIENTS 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 30 The default values are cal culated by the code if this keyword is not given see section 4 2 NO CONSTANT OFFSET 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 44 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt NO_FITTED_OFFSET Instructs the program not to fit the offset value p
21. 1 file contains a title line which is ignored and the next line must contain the ideal AI O bond distance to be used the weighting for this bond re straint e 100 and then the weighting for the tetrahedral angle restraint 300 The following line must contain the ideal bond distance to be used the weighting for this bond restraint and then the weighting for the tetrahedral angle restraint The 1 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 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 of these neighbour files should be generated using the neighbour list program supplied with RMCProfile and described in section 6 1 4 10 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 2 This differs from the SrTiOs restraint in that the network consists of octahedra of two sizes one for the ZrOg one for To use this restraint option 6 needs to be specified in the dat file and poly zro ozr tio and oti files supplied The 1 file contains a title line which is ignored a
22. 6 1 1d 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 e f your input file is a classic version configuration file you will be asked for the names of the atoms e If data2config 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 data2conf ig 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 12 will ask for the element T
23. 99 500 10 636 142 900 3 121 117 500 6 366 105 000 7 864 135 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS 110 607 6 054 0 gt 110 200 4 744 107 200 8 988 CospsaLkane Nnsps Ccsp2aLKENE 106 800 7 465 108 100 7 490 CosPaaLkaNE NNsPa CBENZENE LOCALIZED 102 500 7 465 110 500 7 328 106 400 7 552 HNHAMINE IMINE NNsp3 CBeENZENE LOCALIZED 109 000 7 328 HNHAMINE IMINE Nnsp3 CcspacYCLOBUTANE 108 100 7 490 CospsaLkane Nnsp2 CcspsaLKANE 122 500 9 487 CospsaLkane Nnsp2 Ccsp2aLKENE 119 900 7 864 CospsaLkane Nnsp2 Ccsp2carBonyL 121 100 20 223 Ccspsatkane Nnsp2 Ss SO2SULFONE 110 000 3 745 122 400 2 372 120 400 9 113 2 111 200 5 243 CcsPsaLkaNE NNsP2 Cc oCYCLOBUTANONE 110 000 7 490
24. For users of the Bragg component of RMCProfile data2config will allow you to set up all the Bragg files from the original GSAS files 6 1 1 Command syntax The data2config program is run in the command or shell window by typing a command of the form data2config optional flags filename If you don t have your path 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 When run without any arguments you will get a summary of the command flags and file types More help information can be obtained from the following command and flag One useful first command argument is data2config help The various flags all of which are prefaced with a hyphen and some of which have a following argument are Write the configuration to CIF for viewing by crystal structure sualisation program This enables a check that the configuration is what you expected it to be The output file name has the same root name as the input file but is prepended by the characters new so if the input crystal structure is called sio2 cif the configuration will be written to new sio2 cif crystal Writes a file in the format used by the crystal tool for generation of version 3 configuration files described later The output filename has the extension cfgcom cssr Write the configuration to a CSSR Daresbury Laboratory s Cambridge S
25. 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 19 154 RMCProfile Manual v6 5 2 2 10 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 dat a representative plot is given in Fig 2 4 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 5 0 0 5 10 15 20 25 1 Figure 2 4 A typical equilibrium 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 541 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 gener
26. 5 111 500 3 745 0 0 0 124 300 8 738 CcsreaLkENE CcsPecanBoNvt 7 Oo ccARBONYL 122 000 16 228 c CARBOXYL 124 300 8 738 123 400 16 228 126 500 9 987 2 120 000 8 676 OcsPecanBoNvL CcsPecaRBONYL HEXCEPTONN O S 112 400 8 489 CcspecarsonyL Ccsp2carsonyL DpeuTERIUM 110 600 8 489 CcspacarsonyL Ccsp2caRBONYL Oo cc 0 119 200 9 362 CcspacarsonyL Ccsp2carBONYL Oo c c C C C 121 600 8 863 HexcEPTONN O S Ccsp2caRBONYL HExcEPTONN O S 115 500 8 114 0 0 0 0 107 000 6 866 HexcEPTONN O S CcsP2cARBONYL O0 CCARBONYL 119 200 10 611 HexcEPTONN o s Ccsp2carBonyL Nnsp2 109 300 5 493 HexcEPTONN O S CcsP2CARBONYL F FLUORIDE 104 000 16 728 HexcePTONN O S Ccsp2caRBONYL CICHLORIDE 105 150 15 230 8 108 800 13 981 HexcEPTONN O S C csP2cARBONYL OCARBOXYLATEION 114 900 7 403 HexcEPTONN O S Ccsp2caRBONYL CcsP3cYCLOBUTANE 120 000 6 991 HexcEPTONN O S C csP2cARBONYL OOH O C CARBOXYL 107 000 6 866 HexcEPTONN O S CcsP2caRBONYL Oo cc 0 118 900 7 989 HexceEPTONN O S CcsP2cARBONYL
27. Oo cX HALIDE 110 000 3 995 117 200 9 987 HexcEPTONN O S CcsP2cARBONYL Oo ANHYDRIDE LOCL 101 000 12 483 0 121 500 21 222 134 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS Oo ccarBonyL Ccsp2carBoNYL Nnsp2 124 800 13 357 Oo ccarBonyL Cecsp2caRBONYL CcYCLOPROPANE 122 500 5 742 Oo ccarBonyL Ccsp2caRBONYL CcsP3cYCLOBUTANE 122 500 10 611 Nnsp2 Cesp2carBonyL Nnsp2 112 500 11 235 Fr_LuorIDE CcsP2caRBONYL O0 Cx HALIDE 120 000 21 846 0 120 500 15 479 120 270 10 611 117 400 6 242 120 500 7 989 OcarBoxYLaTEION Ccsp2CcARBONYL OCARBOXYLATEION 129 800 17 876 OoH 0 c CARBOXYL C csp2cARBONYL Oo co H ACID 121 500 21 222 OoH 0 c CARBOXYL C csp2caRBONYL Oo co C ESTER 121 500 21 222 Oo co c o CcsPecangoNv Oo ANHYDRIDE LOCL 119 000 24 967 Oo c c c0c 0 CcsezcanBoNvi Oo ANHYDRIDE DELO 121 000 16 228 CcsPALKvNE CCSPALKYNE 180 000 4 744 180 000 4 182 1
28. 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 overlapping 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 SiOz 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 ne
29. 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 1 58 1 0 500000 0 750000 0 000000 6 1 1 0 59 GI 0 500000 0 500000 0 250000 7 1 1 0 60 CL 0 750000 0 750000 0 250000 8 1 1 0 61 CL 0 750000 0 500000 0 500000 5 1 1 1 62 CL 0 500000 0 750000 0 500000 6 1 1 1 63 CL 0 500000 0 500000 0 750000 Al 1 1 1 64 CL 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 N
30. 115 830 118 100 110 500 116 500 118 500 119 000 120 000 120 200 119 200 110 700 105 000 119 800 104 000 111 200 107 000 120 000 119 000 120 000 126 000 117 000 116 800 116 000 114 600 116 100 107 100 123 500 114 400 5 617 6 616 4 494 6 242 9 987 4 993 4 494 5 418 6 117 6 117 9 987 4 619 6 242 8 988 6 866 4 993 10 611 7 490 4 993 11 859 19 599 19 599 6 242 7 115 6 242 6 616 6 242 4 993 5 617 14 980 4 993 7 240 15 604 6 242 12 483 5 792 8 114 10 611 7 115 133 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS Cosp3aLkane CcsP2carBONYL F FLUORIDE 109 000 24 342 CospsaLkane CcsP2carBoNYL ClcHLoRIDE 110 200 18 101 CcspsaLkane Ccsp2carsonyL BreromiDe 109 300 14 730 CospsaLkane CcsP2carBoNnvL liopIDE 108 890 12 109 CcspaaLKANe Ccsp2cAarRBONYL OCARBOXYLATEION 115 900 9 300 Cosp3aLKaNe Ccsp2caRBONYL O0H 0 C CARBOXYL 110 300 19 349 CcsesaL kaNe CcsezcanBoNvL Oo cc o 122 100 8 988 Cosp3aLKaNe Ccsp2caRBONYL Oo0 co H ACID 123 500 10 611 _ 121 600 3 995 gt 123 000 7 490 Cosp3aLkane CcsP2caRBONYL Oo ANHYDRIDE LOCL 109 000 24 967 Cosp2aLKeNe CcsP2caRBONYL CcsP2ALKENE 114 700 10 611 Cosp2aLkeNe CcsP2caRBONYL CcsP2cARBONYL 120 000 9 987 1
31. 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 50 154 RMCProfile Manual v6 5 2 4 2 NEUTRON AND X RAY COEFFICIENTS 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 2 Neutron and X ray coefficients The neutron coefficients are defined as f cjc b bj where and j label two atom types is the number concentration of atom type and 6 is the coherent scattering length of atom type This is illustrated with the example of The atoms in the configuration are ordered as C The corresponding values of c are 346 646 and 646 respectively The coherent scattering lengths for these elements are 5 922 2 49 6 646 and 9 36 fm respectively However the default units used by RMCProfile require values smaller by a factor of 10 Thu
32. AG3ICOICN 6 Bragg profile background Phase coefficients pressure AMBIENT Coefficients used in Daa ne ef data Ferri to the Bragg pie ated RR Paineen wihoui peak broadening Bragg profile type Bragg profile type Type of profile function to describe the shape of Input Parameters gt Bragg peaks in the Bragg profile data Initial System Recalculate hkl list Flag that determines whether 3 not to recalculate the hk Body of Simulation Flag that determines rmcprofile summary Step 144815 whether or not to swapsried 92422 omlUnits countable e COUR chd dof 43 5586 cmlUnits dimensionless Gon ch sq 52 5687 cmlUnits dimensionless L irf 442468 cmlUnits dimensionless chisa 0 0097 cmlUnits dimensionless Fe Created using ccViz by Toby White me uk See CML Comp for more information Figure 6 1 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 Output rmcprofile Output D t or rmcprofile summary Step 144815 swapstried 92422 cmlUnits countable reciprocal space chi dof 43 5586 cmlUnits dimensionless data sets chig 52 5687 cmiUnits d
33. Allowed values are rmce6f rmc3f and cfg There is default version 35 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE DATA_NOTE 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 DISTANCE_WINDOW Introduces a block of subordinate keywords which provide the distance window constraint information END Indicates that this is the last line to be read 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 FIXED_COORDINATION_CONSTRAINTS Requires an integer which identifies the number of average coordination constraints to be used Is followed by a subordinate keyword to define the parameters Default is to not use this con straint if this keyword is not provided FLAGS Introduces a block of subordinate keywords that switch on off various options IGNORE HISTORY FILE Instructs rmcprofile to ignore any his his6f files present the working directory INPUT CONFIGURATION FORMAT Requires a number that indicates a version for the format of the input configuration file Allowed values are rmc6f rmc3 and cfg There is no default version INVESTIGATOR Requires text concerning the name of the per
34. START POINT 1 49 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE END_POINT 2471 CONSTANT_OFFSET 0 0 WEIGHT 0 5 NO FITTED OFFSET NO FITTED SCALE CONVOLVE V CML gt QOVIA FLAGS NO_MOVEOUT SAVE CONFIGURATIONS NO RESOLUTION CONVOLUTION CSSR V gt 5 gsas2 gt RECALCULATE gt SUPERCELL 6 4 6 gt WEIGHT 0 01 POTENTIALS gt STRETCH 8 5 1 15 Ang STRETCH Co C 5 0 eV 2 0 Ang STRETCH Ag N 6 0 eV 1 5 Ang STRETCH_SEARCH 20 ANGLE Ag 10 eV 180 deg 1 5 1 5 Ang ANGLE 10 ev 90 deg 1 8 1 8 Ang ANGLE_SEARCH 10 deg TEMPERATURE 300 K PLOT pixels 400 colour charcoal zangle 90 0 zrotation 45 0 deg VV This 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 files These data are reproduced within the CML file 2 The atom list here is for the example 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
35. 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 file The main whatever dat file which is the file that controls the 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 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 NEUTRON REAL SPACE DATA 1 33 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt FILENAME ag3cocn6_300k_tr dat gt START POINT 1 END POINT 2000 WEIGHT 0 02 FLAGS SAVE CONFIGURATIONS END You immediately notice the first main rule namely the us
36. VII 1 93 1 88 2 81 UVI 2 075 1 966 2 46 In 111 1 902 1 79 228 Vill 1 743 1 702 2 19 IrV 1 916 1 82 2 30 1 784 1 7 2 16 2 13 1 99 2 52 VV 1 808 1 71 2 16 Lalll 2 172 2 057 2 545 WVI 1 921 1 83 2 27 Li 1 466 1 36 1 91 2014 1 9044 24 Lull 1 971 1 876 2 361 1 985 1 875 2 371 1 693 1 581 2 08 211 1 704 1 62 2 01 Mn Il 1 79 1 698 2 13 ZrIV 1 937 1 854 2 33 Mn 1 76 1 66 2 14 148 154 RMCProfile Manual v6 5 2 APPENDIX D CHANGE LOG Appendix D Change log Version 6 5 v6 5 2 1 Helen started so things back on track and the new changes are 2 Incorporation of bond valence and distance window parameters into the main v6 dat file bvs and dw files no longer needed 3 Fixed and average coordination constraints resurrected and added to the v6 dat file 4 Triplets angle search fixed 5 Move counter no longer resets after 100000 moves 6 Various other bugs fixed 7 X ray example added to tutorial 8 Improvements to the manual while still not complete it s a lot closer v6 5 1 1 Sorry lost track of changes but I think EXAFS was first added here We still need to improve the documentation but this will be in a later release 2 Probably other bug fixes Version 6 4 v6 4 8 1 Computes the bond Kubic harmonic function average values up to 10 149 154 RMCProfile Manual v6 5 2 2 Computes the angle distribution function for the
37. although their func tionality is largely superseded by the more versatile distance window constraints However if one is studying an amorphous material and is using a randomly generated starting configuration it is highly likely that none of the atom pairs obey the proposed distance window and therefore this con straint will fail In these circumstances the coordination constraints are highly useful Options for both fixed coordination constraints where the intent is to drive all of a certain type of atom to have a specific coordination number and average coordination constraints where the average coordi nation number should be for example 4 but as long as this is achieved coordination numbers of 3 or 5 are also acceptable are available The usage of these constraints is discussed in section 4 1 2 It is almost certainly a bad idea to try and use them both at the same time 2 9 Polyhedral restraints Within RMCProfile defined a series of system specific polyhedral restraints The aim of these restraints is to maintain the integrity in terms of connectivity of a polyhedral network during RMC refinement This is achieved by restraints on bond lengths and angles taking into account the atoms which neighbour each other in coordination polyhedra A full description of these restraints can be found in section 4 10 While the polyhedral restraints are not generic they are not limited to systems of the named compo sition but can be
38. cfg Or his files containing the raw data no constrains on the name files to manage the Bragg scattering bragg back inst and hk1 and files concerned with restraints dw bvs bonds and triplets Many of these files will have the same stem name but different extension tags For example if we were performing an RMC simulation on the crystalline phase of methane we might have the following input files optional unless stated otherwise methane dat containing the key data required to control the RMC simulation compulsory sec tion 4 1 methane rmc6f containing the atomic configuration in fractional or cartesian coordinates respec tively If using classic format the file name to be used is methane c g and you also have the option to call this methane rmc3 if using Version 6 dat file with classic configuration format This file is compulsory unless methane his6f is present section 4 11 methane his6f contains the latest configuration and the pair distribution functions as generated by the most recent run and if this is present it will be used in preference to methane rmc6 If using the classic file format this file is called methane his subsection 4 11 2 methane bragg containing the Bragg diffraction data section 4 13 methane back containing parameters to describe the shape of the background in the Bragg diffraction data section 4 13 Actually we will see later that this behaviour ca
39. nag file contains a list of silver neighbours around each nitrogen atom and the agn file contains list of the nitrogren neighbours around each silver atom All of these neighbour files should be generated using the neighbour 1185 program supplied with RMCProfile and described in section 6 1 4 10 13 The Zn CN 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 SiO restraint in that the network consist of tetrahedra link by two bridge atoms 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 file and zncn czn nzn and nc files supplied The 74 154 RMCProfile Manual v6 5 2 4 11 RMC VERSION 6 FORMAT CONFIGURATION FILES 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 100 and then the weighting for the tetrahedral angle restraint 300 The following line must contain the ideal 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
40. the maximum values of the Miller in dices h and 6 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 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 RECALCULATE Recalculate the list of reflections to use The default setting is not to recalculate 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 WEIGHT Parameter to weight the contribution of the Bragg pro file to the Monte Carlo simulation BVS ATOM Give the element symbols for each atom in the config uration in the same order as defined in the configura tion file this is essentially a duplication of the ATOMS keyword but unfortunately is necessary OXID Give the oxidation states for the atoms in the same order as above WEIGHTS Give appropriate weightings for the bond valenc
41. 104 2 17 1 032 CcsPsALKANE S S SULFIDE 1 80 1 440 CcsP3ALKANE S gt 5 SULFONIUM 1 82 1 542 CcsPaALKANE S gt S OSULFOXIDE 1 80 1 416 gt SOPSULFONE 1 77 1 488 CcspsaLkANE SIsILANE 1 88 1 464 1 51 2 400 gt 1 84 1 411 CcsPsaLkaNE B gt BTRIGONAL 1 58 2 160 CcsesaLkaNE C RADICAL 1 50 2 496 CcsesaL kaNE GeGERMANIUM 1 95 1 305 2 15 1 019 2 24 0 912 CcspaaLKANE S SELENIUM 1 95 1 286 lerELLURIUM 214 1 296 CcsPaaLkaNE DoeurERIUM 111 2 275 CocsPsaLkaNE NN C PYR DELOCLZD 143 2 400 CcsPaaLkANE CcsP2cvcLoPROPENE 1 50 2 112 CcsPaALKANENNSPSAMMONIUM 1 51 2 051 CcospsaLkane Nnsp2PYRROLeE 1 49 2 030 2 1 42 2 592 CcsPsaLkaNE N NOAZOXY LOCAL 148 2 496 1 50 2 640 Cosp3aLKANE CBENZENE LOCALIZED 1 50 3 024 CcsesaLkaNE CcsPscvcLoBUTANE 1 52 2 155 2 1 50 3 024 149 3 552 CcsPaALKANE CKETONIUMCARBON 1 50 2 304 CosPsALKANE N NIMINE LOCALZD 1 44 2 400 Cosp3aLKANE OOH 0 C CARBOXYL 1 41 2 736 CosPsaLkaNE NN AZOXY LOCAL 1 45 2 150 121 154 RMCProfile Manual v6 5 2 2 1 BOND STRETCHING TE
42. 2 gt 2 6 9215 gt lt aequnwN eueu 6 gt lt gt gt gt 283 gt gt wezed gt lt gt lt gt lt 002 3 3 4 lt 9 OO 59 lt 0 9 JUS UCD UOTSISA lt 2 4 4 lt 2 4 939pejew eueu gt Ga TSX 3Xe3 9dA4 9 439 1 gt lt 8 40 gt 3 3 gt gt 26 154 2 13 XML OUTPUT FILES RMCProfile Manual v6 5
43. 2 2 2 Introduces a block of data concerning set of neutron derived real space data 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 2 EUTRON 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 De fault units are Default value is the the value automatically calculated from the configuration file and this will always override any value given with this keyword 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 section 4 10 Default is to not use this constraint if this keyword is not pro vided
44. 2 The refinement will give an absolute scale factor that is required as input for the Bragg part of RMC 11 154 Manual v6 5 2 2 4 DISTANCE WINDOW CONSTRAINTS 3 The refinement will give parameters for the background function to enable the Bragg peaks to be accurately subtracted from the diffraction pattern 4 The refinement will give parameters for the experimental resolution function which are used in the RMC treatement of the Bragg profile In practice the Bragg part of RMCProfile is closely tied to the functions used in the GSAS pro gram and thus we recommend that GSAS be used for the Rietveld refinement Users may of course use their preferred refinement packages for their Rietveld work but at the present time it is necessary to convert the output into GSAS format in order for RMCProfile to read it The user will be required to give the Bragg diffraction profile at the present time RMCProfile will only use data from a single bank of detectors from a spallation neutron source background parameters the scale parameter the parameters for the resolution function and the upper Q or lower d limit of the diffraction data to be used 2 4 Distance window constraints The distance window constraint is an extension of the standard closest approach constraint in RMC with two significant enhancements First in addition to specifying the closest two atom types can come together you can also specify the furthest away
45. 4 1 January 2010 Title KCN CCR II at 250K I 12Wx34H chop 19302 1939 Generating user martin File directory Users martin Research rmc KCN 2 Data date 17 2003 12 04 47 stog date 25 01 2010 stog time 12 11 27 Number of points 2000 2 00000000000000004 002 13 271486492010869 0 73834056742191556 4 00000000000000008 002 8 5875318972803303 0 56286299993679112 5 99999999999999978 002 2 9343881244971763 0 35405575737765133 8 00000000000000017 002 1 5829247982417609 0 20558527999260373 0 10000000000000001 3 6272129637947250 0 16511124249615863 0 12000000000000000 3 1324692439799078 0 15321102691071234 0 14000000000000001 1 1215681925009062 0 12718942545392448 Again are using metadata with this file 5 2 2 Data file In the input data file the scattering data are handled using the following keyword block NEUTRON REAL SPACE DATA 1 FILENAME GEM12285 gr DATA TYPE G r FIT TYPE D r START POINT 1 END POINT 3000 CONSTANT OFFSET 0 0000 WEIGH 0 01 NO FITTED OFFSET STOG The key points from this example are 1 The PDF data file gives the data in G r format but we are using the D r function for the RMC analysis In this format the errors are more or less equal for each point 90 154 RMCProfile Manual v6 5 2 5 3 EXAMPLE OF USING THE BRAGG PROFILE
46. 5026 102 000 22 470 Cosp3aLKANE S gt 80250 0 5 106 000 9 238 9 gt soesuLFoNE Oo ccARBONYL 106 900 13 732 8 gt 80250 2 103 000 9 987 gt so2suLFONE CcsP2ALKENE 102 100 24 717 Ccsp2aLkene S gt 8028 108 100 24 592 0 879 8028 101 500 6 991 0 879 8028 2 98 000 7 490 Oo ccARBONYL S gt 80250 119 500 18 538 Oo ccaRBONYL S gt so2suLFONE Nnsp2 108 000 21 222 5151 109 500 5 992 CCSP2ALKENE 110 200 4 993 5 109 300 4 993 CospsaLkANESisitane Oco H c 0 c 0 0 108 000 6 866 Ccsp3aLkANE SisiLane SisiLane 109 000 5 617 CcsesaLkaNE SisiLANE CCYCLOPROPANE 110 200 6 616 CcsesaLkaNE SisiLANE CCSPSCYCLOBUTANE 109 500 6 616 CcsreaLkENE SisiLANE CCsP2ALKENE 104 500 7 490 Cosp2aLKENE SIsiLANE HEXCEPTONN O S 109 500 6 866 Cosp2aLKENE SisiLanE Oco H c_o c 0 0 109 500 6 242 5 961 110 200 4 993 3 1 5 106 500 5 742 8
47. 58 58 58 68 70 70 75 79 80 82 86 RMCProfile Manual v6 5 2 5 Examples 5 1 Using scattering data 5 2 Using PDF data 5 3 Example of using the Bragg profile 5 4 Example of using potentials 5 5 Example of using Bond valence sum 5 6 Example of using constraints 5 7 Example of using polyhedral restraints 5 8 Example of using magnetism 5 9 Example of using EXAFS data 5 10 Example of using X ray data 6 Tools for data preparation and analysis 61 Data preparation tools 6 2 analysis tools 6 3 CML based analysis tools A Basic theory of total scattering 1 1 Total scattering 1 2 lsotropic averaging 13 method Suggested values for interatomic potentials 2 1 Bond stretching terms 2 2 Bond bending terms C Bond valence parameters 3 1 Values for bond valence sum calculation D Change log E References CONTENTS 88 88 90 91 92 94 95 96 97 98 98 99 99 107 108 114 114 117 118 120 120 127 146 146 149 153 RMCProfile Manual v6 5 2 CHAPTER 1 INTRODUCTION Chapter 1 Introduction 11 We know you don t read manuals Very briefly RMCProfile is an implementation of the Reverse Monte Carlo method 1 RMCProfile is based on the original code for RMC but significantly amended and extended to give new capabilities and to take account of more recent programming and informatics standards If you just want get things running please just look for the rmcprofile tutorial pdf
48. Difference between fitted and experiment Bragg profile Difference between fitted and experiment PDF 1 Difference between fitted and experiment scattering function 1 d spacing for Bragg profile Experimental Bragg profile data Experimental total PDF for dataset 1 Experimental scattering data for dataset 1 Flag Y N to denote whether hkl array was recalculated Metadata item on the investigators Metadata keywords Matrix of lattice vectors Maximum distances in distance windows Maximum move allowed per atom type Minimum distances in distance windows Neutron coefficients for PDF dataset 1 Neutron coefficients for scattering dataset 1 Number of neutron PDF datasets Number of neutron scattering datasets Number of average coordination constraints Number of coordination constraints Number density Number of different atomic species Numbers of atoms of each type Number of X ray scattering datasets Y N values to denote application of offsets to data Constant offsets applied to data Partial PDF for atom pair 1 Metadata item on sample phase Metadata item on sample pressure Number of steps between printing Array of scattering vectors for scattering data Partial iQ Q data for atom pair 1 Array of distances used in PDF functions Y N values to denote automatic data renormalisation Fitted Bragg profile Fitted PDF function for dataset 1 Fitted scattering function for dataset 1 Metadata note about the RMC simulation
49. HexcEPTONN O S CcsP2cYCLOBUTENE 1 10 2 472 HexCEPTONN O S CKETONIUMCARBON 1 09 2 448 HexcEProNN o s CHcrERROCENEH 1 10 2 472 0 5 gt 1 40 1 574 HexcEPTONN O S 9 gt 80250 1 35 1 788 1 45 1 896 0 1 64 2 424 0 0 95 3 662 0 0 97 3 432 0 gt 1 61 1 392 0 0 gt 1 36 2 217 0 0 1 42 1 344 0 135 2 880 0 97 3 456 0 0 gt 1 60 2 544 Oo ccARBONYL S gt S OSULFOXIDE 1 49 3 408 8 gt 80280 1 44 4 521 Oo ccanBoNvL N NOAZOXY LOCAL 1 27 5 183 Oo ccarsonyL Nnitro 1 22 3 600 Oo ccarsonyL Cc ocYCLOBUTANONE 1 20 4 871 Oo ccarBony Cc ocyYcLOPROPANONE 1 20 5 481 1 17 5 039 Oo ccanBoNvL P P oPHOSPHATE 1 49 4271 Oo ccARBONYL S gt 8028 1 46 4 164 Nuspa HNHAMINE IMINE 1 01 3 081 BENZENE LOCALIZED 1 38 3 033 1 45 2 544 124 154 RMCProfile Manual v6 5 2 2 1 BOND STRETCHING TERMS
50. K Note that this value will be over ridden by the value of sample temperature provided in the metadata input SWAP 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 SWAP ATOMS List the numbers of atoms to be swapped 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 47 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt SWAP_TUNE Tune the swapping probability Default is not to tune XRAY RECIPROCAL SPACE DATA DATA TYPE Reserved for the type of data the only option today is F Q 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 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 subordi
51. RMCPROFILE INTRODUCTION The method gives a snapshot view 10 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 albeit 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 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 average positions of atoms and their mean
52. Sample extracts of an RMCProfile CML file are shown in Figures 2 7 and 2 8 You can see that each item of date is properly described within the CML file For example in Figure 2 7 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 2 7 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 2 7 you can also see a set of 24 154 RMCProfile Manual v6 5 2 2 13 XML OUTPUT FILES input parameters that are nested within the lt parameterList gt 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 where in Figure 2 7 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 2 7 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
53. a dictionary item describing the parameter a name The data items are accompanied by a description of the units Figure 2 8 shows actual data generated These are contained within lt module gt tags which are defined for different tasks or roles The examples in Figure 2 8 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 functions and comparison of data and calculated functions for plotting with the ccviz tool described below As a prelude to the more detailed description given in section 6 3 we note that there are several applications that stem from using XML data representation In general terms XML files can easily be transformed to other representations including XHTML This is exploited in the ccviz tool that is described in subsection 6 3 1 and which is bundled with RMCProfile A second application called summon also supplied with the RMCProfile package and described in subsection 6 3 2 enables extraction of information from an XML file without having to scroll through the file Both tools require Python to be available on the computer being used and both work from the command line 25 154 2 13 XML OUTPUT FILES RMCProfile Manual v6 5 2 131 pue
54. around 1 10 5 seem to work best Outside of this range you risk either the constraint being ignored completely or the data being ignored in favour of the constraint In the following example it is specified that 100 of atom number 1 should have a coordination number of 4 and that 100 of atom 2 should have a coordination number of 2 This sort of setup would be suitable for a tetrahedral network such as 5102 FIXED_COORDINATION_CONSTRAINTS 2 gt 1 2 0 5 2 0 4 1 0 0 00001 gt CSTR2 2 1 0 5 2 0 2 1 0 0 00001 An average coordination constraint will allow individual coordination numbers to differ from the specified value as long as the average is as desired AVERAGE_COORDINATION_CONSTRAINTS 1 gt CAVSTR1 1 2 0 5 2 0 4 0 0 00001 5 7 Example of using polyhedral restraints This example shows what is required to use the SiO polyhedral restraint Please note that at the present time you will need to have your configuration in the classic style with extension cfg for the polyhedral restraints to work In the dat file the following line must appear POLYHEDRAL RESTRAINT 1 This tells RMCProfile that you are using polyhedral restraint number 1 the SiO restraint which maintains a network of linked tetrahedra through restraints on bond angle and length The restraint requires several simple auxiliary files to be present in your working directory and with the same st
55. bond angles defined in the input data 3 Calculates the mean bond distances and angles 4 Asmall number of bug fixes 5 Writes more data to the output CML file v6 4 7 1 Ability to read directly data files generated by the STOG program used for Fourier transform of the scattering data 2 Generates spherical harmonics of the bond orientations and gives mean and mean square values as output files 3 Inclusion of TGNORE_HISTORY_FILE keyword 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 theGudrun data reduction and transformation package Ability to read supercell information from the file 4 Ability to read the range of d spacings from the dat file and for the code to generate the range h 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 from 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 150 154 RMCProfile Manua
56. central atoms that you want to have this coordination number e g 1 0 and the weighting for this constraint e g 0 0001 the smaller this value the harder it is for atoms in the correct coor dination to wander away from it The 1 refers to this being concerned with the first fixed coordination con straint Duplicate this subordinate keyword and ap pend the appropriate number e g gt CSTR2 if you have more than one constraint 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 gt MOVEOUT 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 gt NO_MOVEOUT 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 gt NO_RESOLUTION_CONVOLUTION 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 42 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt NO SAVE CONFIGURATIONS Instruct the program not to output a separate configu rat
57. data can be accompanied by two other files The first is the file containing the instrument resolution function extracted directly from the GSAS output file 1456 130 0 3300000 3 020000 17 98000 0 000000 00 0 381440 00 0 322500 02 0 532200 02 0 000000 00 0 200492 03 0 000000 00 0 000000 00 0 146638 02 0 000000 00 0 000000 00 0 000000 00 2 4883 270 1 960000 7 080000 63 62000 0 000000 0 00 0 381443 00 0 322488 02 0 532215 02 0 000000 00 0 265473E 03 0 000000 00 0 000000 00 0 101245 02 0 000000 00 0 000000 00 0 000000 00 6681 000 5 230000 2 120000 91 37000 0 000000 00 0 381440 00 0 322500 02 0 532200 02 0 000000 00 0 135144 03 0 000000 00 0 000000 00 0 943758 01 0 000000 00 0 000000 00 0 000000 00 4 9087 750 9 690000 5 120000 154 4600 0 000000 00 0 381443 00 0 322488 02 0 532215 0 223010 02 0 949869 02 0 000000E 00 0 000000 00 0 981154 01 0 000000 00 0 000000 00 0 000000 00 02 LH Here we give data for four banks even though the Bragg diffraction data can only use one bank The second file is the list of background parameters 5 3 2 Data file In the input data file the Bragg profile is handled using the following keyword block BRAGG BRAGG SHAPE GSAS2 WEIGHT 01 gt RECALCULATE gt DMIN 0 9 The fitted function is shown in Figure 5 3 In this case agre
58. 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 608086 05 39 98 0 002873718 40 00 0 004977553 4 12 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 79 154 Manual v6 5 2 4 13 BRAGG SCATTERING traditional format The subordinate keyword GUDRUN needs to be provided with the NEUTRON_REAL_SPACE_DA and NEUTRON RECIPROCAL SPACE DATA keyword blocks The file format looks something like the following for the scattering function 4 GEM12234 mdcs01 KCN in at 20K I 12Wx34H chop 19302 0o0f 1 2502 10 DAK MTD 15 2003 02 14 23 spec bad groups_def dat 6 1 0 1700000 02 0 0000000 400 0 1456720 01 0 0000000 00 0 0000000 00 0 5096614E 02 0 0000000E 00 0 0000000 00 0 9269717E 02 0 0000000 00 0 3000000E 01 0 0000000 00 0 0000000 00 0 5000000 01 0 0000000 00 0 0000000E 00 0 8900000 00 0 4750513 00 0 1049418 02 0 9100000 00 0 4789928 00 0 1090569 02 0 9300
59. each direction to be as close to the provided value as possible and avoid the need to be asked the questions sort 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 supercell Generate a supercell of the input crystal unit cell by multiplying each unit cell vector by an integer The set of integers are provided within a pair of square brackets Any number of options can be selected for example 101 154 RMCProfile Manual v6 5 2 6 1 DATA PREPARATION TOOLS data2config cssr rmc6f size 50 sort NaCl cif will produce an RMC configuration file from an initial CIF file for sodium chloride with approximate dimension 50 in each direction ordered by atom type in order of atomic number and also giving a CSSR file for drawing with appropriate crystal visualisation software data2config rmc6f sort rect quartz tbl will produce an RMC configuration of quartz from a GSAS output file again with atoms sorted and with orthogonal axes rather than the crystallographic hexagonal axes but with a supercell yet to be provided by the user in response to questions given at the terminal and data2config rmc6f sort nano 40 TiO2 cif will produce a configuration containing a single spherical nanoparticle of with radius 40 6 1 1b Allowed crystal structure file types The allowed input file types are denoted by th
60. files should be generated using the neighbour_list program supplied with RMCProfile and described in section 6 1 4 10 4 The 5 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 To use this restraint option 4 needs to be specified inthe aat poly sfand fs files supplied The poly file contains a title line which is ignored and the next line must contain the ideal 5 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 sf file contains a list of fluorine neighbours around each sulphur atom and the s 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 6 1 4 10 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 AIO and one for To use this restraint option 5 needs to be specified in the dat and poly alo oal po and op files supplied The
61. flight neutron diffraction where total scattering data to Qmax 50 1 is routinely ac cessible This is achieved through the availability of short wavelength neutrons and because the neutron nucleus interaction does not introduce a fall off in intensity at high Q in contrast to X ray diffraction where the form factor significantly suppresses scattering at high Q More recently however diffraction instruments using high energy X rays from third generation syn chrotron sources have provided total scattering data to 35 and there are also some laboratory X ray diffractometers based on silver or molybdenum anode sources that can provide data to Qnax 20 24 The data will typically need to be collected for longer in order to measure the weaker broader diffuse scattering with sufficient statistics Sources of background should be minimised and measured in order to make a robust sub traction This typically involves measuring in addition to the sample the empty sample can or capillary empty sample environment and empty diffractometer all in the same experimental configuration The data need to be normalised accurately and placed on an absolute scale This is achieved for neutron diffraction through the measurement of a vanadium sample of similar dimensions to the sample an equivalent measurement is not possible for X ray diffraction and a number of routines exist to facilitate accurate scaling of the data see for example
62. focuses only on the atomic distribution which in practice usually means obtaining the mean positions of the atoms and their associated distribution function which is usually defined as a Gaussian function with a width in three dimensional spaced defined by an ellipsoid function with six parameters defining its shape and orientation Bragg diffraction alone contains no information on the correlation between neighbouring atoms which is the information contained within the diffuse scattering component of total scattering By explicit treatment of the Bragg scattering we give more weight to the distribution of atomic positions and allow the treatment of the total scattering to focus more on the correlated motions of the atoms Furthermore since the Bragg peaks are assigned a set of Miller indices which reflect the fact that the scattering vectors associated with the Bragg peaks are vectors in three dimensional space Thus inclusion of this information puts something of the three dimensional nature of the data into the RMC model even though the data are collected in one dimensional mode The experiments are typically performed using powder diffraction It is important that for each data set run through RMC there will have been a prior Rietveld refinement performed There are four reasons for this 1 The refinement will give the best lattice parameters consistent with the data and which should be used in generating the initial atomic configuration
63. 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 magnetic structure of the well known antiferro magnet MnO At temperatures below 120K the 3 magnetic moments of the 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 2 1 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 2 1 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 ATOMEYE is given as mnoeye cfg It is worth taking 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 2 2 A set of 256 random spin orientations are given in the file mno_spin cfg One method
64. independent extraction of dynamical information from powder diffraction data Physical Review B 72 art no 214304 15 pp 2005 20 A L Goodwin 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 21 A L Goodwin S A T Redfern M T Dove D A Keen M G Tucker Ferroelectric nanoscale domains the 905 phase transition in SrSnO3 A neutron total scattering study Physical Review B 76 art no 174114 11 pp 2007 154 154
65. molecular mechanics force field model we set 2 55 for all atom pairs We can write a simple expansion of the Morse potential to lowest order Da r rg 4 22 If you prefer to work with this type of quadratic expression but expressed in the following way n 4 23 the association between k D and is clear 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 A set of recommended values for the parameters taken from the MM3 and MM3 protein databases are given in Table B 1 and Table B 2 respectively in Appendix B 4 7 2 Bond angle potentials We use a simple harmonic cosine potential to describe the energy associated with bending of bonds i E 5K cos cos 00 4 24 where 0 is the instantaneous bond angle and is the set angle This equation be expanded to yield E 2K sin gin 00 m 4 25 aK sinf 0o 0 where the angles defined units of radians rather than degrees As with the bond stretching potential we recommend the use of realistic values of the parameter Values of sin for some common bonds are given in Table and Table B 4 taken from the and protein databases respectively in Appendix B 59 154 RMCProfile Manual v6 5 2 4 7 USING POTENTIALS 4 7 3 The main data file Consider the following example f
66. of visu alising 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 17 154 Manual v6 5 2 2 10 MAGNETIC STRUCTURE MODELLING Figure 2 1 The antiferromagnetic structure of MnO Mn and O atoms are shown as large light grey and small dark grey spheres respectively X mnoeye Figure 2 2 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 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 2 2 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
67. periodic boundaries Unlike other techniques it is not appropriate to consider contributions to the pair distribution function for interatomic distances that extend beyond half way to the the nearest replica generated by the periodic boundaries Thus the configuration needs to be large enough for the pair distribution function to be defined to a useful distance But against this is balanced the fact that the more atoms you have the more degrees of freedom are available to fit the data which may not be a good thing Moreover the more atoms you have the longer the time the RMC simulation will take to reach convergence to a satisfactory result Thus our experience is that a few thousand atoms is typically a good size to work with The starting point for RMCProfile is to generate an initial configuration of atoms RMCProfile expects this configuration to be defined by a box with periodic boundary conditions and a given size together with a list of constituent atoms and their positions within the box 2 12 2 Crystalline materials We provide a number of tools to enable the user to generate an initial configuration of atoms from a trial crystal structure For example we anticipate that many people will start from a crystal struc ture provided in the standard CIF format used by crystallographers or perhaps with a TBL file generated by the GSAS Rietveld refinement code The data2config tool will use the information contained within these files to gen
68. r and high Q parts defines this in normalised form which we call Shorm Q in equation 4 19 below 53 154 Manual v6 5 2 4 3 USING EXPERIMENTAL DATA 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 D r 0 4 x 0 4 13 2 0 0 x 4 14 4 3 4 Normalised functions RMCProfile also allows the use of normalised functions For the PDFs we can defined these as 2 2 Gnorm r any 4 ew 4 15 2 2 D r 4np 7 4 4 16 1 1 with limiting values 0 1 0 0 0 2 CNN TI 1 4 17 7 0 2 r Dnaom r 09 O 0 0 Tnom r 09 4 18 Normalised scattering functions can be defined as 2 norm Q Fnorm Q 00 Snorm Q S Q ss 4 19 with limiting cases 4Note 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 0 54 154 RMCProfile Manual v6 5 2 norm Q gt 0 1 2 Shorm Q Cx 0 1 cb 2
69. 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 5 quartz 3 and cristobalite 4 If you take the crystal structure and calculate the distance between the aver age positions of the closest silicon and oxygen atoms you get a value of around 1 55 Often this distance is associated with the bond length However the PDF which is a true measure of the aver age instantaneous bond length gives an Si O distance of 1 61 The difference between the dis tance 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 fluc tuations 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 3 Introduction to RMCProfile 1 3 1 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 B
70. 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 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 21 154 RMCProfile Manual v6 5 2 2 10 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 2 6 which in this case shows that the spins are aligned parallel and antiparallel to an axis very close to 112 NS Figure 2 6 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 prod
71. the GudrunX manual 9 154 RMCProfile Manual v6 5 2 2 2 FITTING PDF DATA Fortunately there are a number of packages notably Gudrun and Gudrunx which treat the ex perimental data for background absorption multiple scattering etc and produce normalised total scattering data so provided a careful experiment has been carried out there should only be a small overhead in producing total scattering data over a standard powder diffraction pattern RMCProfile will fit total scattering data in both reciprocal space and in real space i e both total scattering structure factors and pair distribution functions It may initially appear curious that the same data can be used in two different ways However experience has shown that it is beneficial to fit both the reciprocal and real space data together since each function emphasises different aspects of the structure the pair distribution function highlights structure at short distances whereas the scattering data are weighted more strongly to the longer range structure Details about these different functions and their forms can be found in section 4 3 2 2 Fitting experimental pair distribution function data As discussed above RMCProfile exploits separately the information contained in the total scat tering data measured in reciprocal space and the pair distribution function PDF which is a function defined in real space As shown in the equations described in section 4 3 the PDF is o
72. 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 dr This function will have peaks corresponding to specific sets of interatomic distances For example a material containing SiO tetrahedra there will be a peak corresponding to the Si O bond at 1 6 and peak corresponding to the bond at 2 3 Each partial g r will be zero for all r below the shortest interatomic distances and will tend to value of 1 at large r Thus we can rewrite Q 9 So 18 sin Qr Qr CmCnbmbn f Arr 1 19 m n 0 where Cm and are the proportions of atoms type m n respectively is the number density Sy is determined by the average density and gives scattering only in the experimentally inaccessible limit Q O 117 154 RMCProfile Manual v6 5 2 1 3 RMC METHOD 1 3 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 primary ex perimental data being total scatter
73. these then we have supplied a basic version from the Cygwin distribution called basic_X_server and this should be sufficient for the RMCProfile tools Alternatively the program Xming is freely available on the and is very satisfactory If you use Mac OS X or Linux Unix you are already set and ready to go 6 1 1 data2config the configuration preparation tool This program will enable you to create a configuration file for RMCProfile 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 101 files known to crystallographers and outputs include the classic generation 3 configuration files as well as the easier to read version 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 An alternative if slightly more labour intensive method uses 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 http www straightrunning com XmingNotes 99 154 RMCProfile Manual v6 5 2 6 1 DATA PREPARATION TOOLS
74. 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 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 for both 2 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 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 This might not work at low temper
75. two atom types are allowed to move apart In this way you define windows or configuration space in which the atoms are allowed to move Secondly the distance window constraint is formulated such that atom neighbours are re tained during an RMCProfile run A network can thus be generated between atoms using the distance window constraints that will retain the overall topology or local molecular topology of the initial model When RMCProfile 1 first run a neighbour list of all the atoms that fit within the distance windows is generated and this list remains the same unless deleted This means that the window sizes can be expanded or reduced later but the atoms being constrained stays the same To use the distance window constraint it is no longer necessary to have a separate dw file although this will still work Instead use the DISTANCE WINDOW keyword the main Version 6 dat file The required information is detailed later in 4 1 2 It is currently not possible to use this constraint with a classic format input file Once run RMCProfile will 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 12 154 RMCProfile Manual v6 5 2 2 5 INTERATOMIC POTENTIALS 2 5 Interatomic potentials In principle the
76. 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 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 55 178 96 74 56 179 70 71 58 180 77 73 55 In many ways this looks very similar to the configuration file format Extensions to the configuration file are most
77. 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 4 7 5 The triplets file The 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 ZnC4 Number of atoms 10 Number of bonds 2 Number of triplets Z2 Zn 1 2 101 C 102 C 101 C 103 101 C 104 101 105 4 Zn l 220 lt gt 01 C 22210 101 1 Zn 102 1 7 103 1 7 104 1 Zn 105 4 lt snip gt 101 2 a 1 Any 201 101 C 2 201 C Z 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 exis
78. with the details 4 14 RMCProfile version 3 classic files In this section we describe the input files required when running RMCProfile the version clas sic mode In most cases we recommend using the new version 6 approach described previously especially for the dat file as this provides access to more functionality 16This is the volume GSAS used to calculate the total scale for the data so has to be the same as value in the EXP file This of course should be the same as the unitcell volume used to build the configuration You may wonder what happened to versions 4 5 The answer is that as the code developed through versions 4 and 5 the input file format remained unchanged 82 154 RMCProfile Manual v6 5 2 4 14 RMCPROFILE VERSION 3 FILES 4 14 1 The dat file This is main control file from here everything you want RMCProfile to do 15 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 0 05 0 1 maximum move 0 020 spacing false whether to use moveout option false collect configurations 1000 step for printing 2400 60 Time limit step for saving 130 No of g r neutron X ray sf6 190k gr 1 1500 0 0 00165 03942 23486 0 05 false sf6190kbanklconv29p42rmc dat 1 3000 0 00165 03942 23486 0 01 false false sf6190kbank2conv29p42rmc da
79. 0 118 000 115 500 118 800 118 100 118 800 116 000 122 000 127 800 120 000 121 457 119 100 120 000 121 000 119 000 119 500 117 000 124 200 115 200 121 000 120 590 118 000 119 700 120 000 117 000 120 000 119 500 119 000 116 400 117 000 109 000 113 000 112 600 112 100 112 600 106 000 119 500 120 000 120 000 7 490 6 242 10 111 8 114 5 617 5 118 12 483 3 995 5 867 4 744 8 801 3 121 6 117 12 109 8 239 13 107 7 240 16 852 12 483 9 487 12 483 9 362 8 738 7 864 6 242 6 242 3 745 5 617 6 741 6 741 3 745 8 863 6 866 6 991 5 617 9 737 6 554 6 117 6 366 RMCProfile Manual v6 5 2 HeXCEPTONN O S CcsP2a HeXCEPTONN O S CcsP2a HeEXCEPTONN O S CcsP2A HeEXCEPTONN O S CcsP2a 0 5 0 5 0 5 0 5 0 5 0 5 2 2 2 HeXCEPTONN O S CcsP2a HexcCEPTONN O S CcsP2a 5 2 LKENE DDEUTERIUM LKENE NN c PYR DELOCLZD LKENE Ccsp2cYCLOPROPENE LKENE NNsP2PYRROLE LKENE OosP2FURAN LKENE SSSP2THIOPHENE LKENE N NOAZOXY LOCAL LKENE CBENZENE LOCALIZED LKENE Ccsp2cYCLOBUTENE LKENE N _NIMINE LOCALZD LKEN
80. 0 000 5 742 CospscvcLoBUTANE CcsPacvcLoBUTANE CCsP3CYCLOBUTANE 109 500 8 364 Cosp2cvcLoBurENE CcsPscvcLoBUTANE CcsPecvcioBurENE 113 200 6 741 CocsPaaLkaNE CcsPocvcLoBUTENE CCsP3CYCLOBUTANE 115 200 6 741 2 2 122 300 5 867 2 2 127 800 9 487 2 2 2 127 200 9 487 0 8 117 500 6 117 HeXCEPTONN O S CcsP2cYCLOBUTENE C cSP2CYCLOBUTENE 120 000 6 117 CospecycLopuTENe CcsP2cYCLOBUTENE Ccsp2cycLoBuTENE 121 700 9 487 0 0 126 000 12 483 135 100 6 866 Nusp2 Cc ocvcLoBUTANONE OO CN AMIDE 125 800 13 107 CospscvcLoBUraNE Cc ocvcLoBUTANONE OO0 CN AMIDE 125 000 8 114 1 126 000 12 483 Oo ccarsonyL Cc ocYCLOPROPANONE CCYCLOPROPANE 143 600 5 742 Cosp3aLKANE OKkETONIUMOXYGEN CKETONIUMCARBON 113 900 9 113 Cosp3aLKANE CKETONIUMCARBON CCSPSALKANE 107 700 3 995 5
81. 0 24898 0 50000 0 50000 0 50000 0 75102 0 50000 0 50000 0 24898 0 sf6 190k cfg 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 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 RMCProfile 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 li
82. 0 9 487 121 700 9 487 120 000 5 368 120 000 7 490 120 000 6 117 NGuanidinium C Guanidinium NGuanidinium 120 000 4 993 Calkane Csp3 CAlkene His TrpC C CPhenyl 122 300 5 867 CAlkane Csp3 CAlkene His TipC C CAlkene His pc c 122 300 5 867 Catkane Csp3 C alkene His TrpC C N imidazolium 120 000 5 368 CPhenyr CAlkene His TrpC C C Alkene His TrpC C 122 000 9 487 Calkene His TrpC C C alkene His TrpC C N pyrrole 120 000 5 368 Catkene His TrpC C Calkene His TrpC C Nimidazolium 120 000 9 987 Calkene His TrpC C Calkene His TipC C HHydrogen cH 120 000 6 117 Neyrrole Calkene His TrpC C H Hydrogen CH 113 500 4 993 Nimidazolium C alkene His TrpC C H Hydrogen CH 113 500 4 993 Nimidazolium C Imidazolium NC N NImidazolium 120 000 4 993 Nimidazolium C Imidazolium NC N H Hydrogen CH 120 000 4 993 C Alkane Csp3 NAmide C Alkane Csp3 122 500 9 487 Catkane Csp3 Namide C amide 121 100 20 223 Catkane Csp3 Namide Hamide 122 400 2 372 Camide Namide Hamide 118 500 7 240 Hamide Namide Hamide 123 000 5 118 Catkane Csp3 Nammonium C alkane Csp3 108 600 7 864 Catkane Csp3 Nammonium Hammonium 109 470 6 242 Hammonium Nammonium Hammonium 104 500 6 24
83. 0 eV 109 471 deg 1 45 1 45 Ang gt ANGLE Zr O 20 0 eV 90 0 deg 2 05 2 05 Ang gt ANGLE_SEARCH 10 deg gt TEMPERATURE 800 K gt angle_histogram dangle 5 deg Here we have stretching parameters for both Zr O and bonds and angle potentials for the O Zr O angles within the 2706 octahedra and the angles within the PO tetrahedra In this case also we are selecting an angle step for the construction of the bond orientation distribution functions that are automatically calculated Pullng together the examples discussed in the previous sections Figure 5 4 shows a single layer of atoms taken from a configuration of the disordered phase of KCN 93 154 RMCProfile Manual v6 5 2 5 5 EXAMPLE OF USING BOND VALENCE SUM 89 9 6 6 9 6 7 6 9 6 9 o 707 e 9 9 tete 19 9 9 Le 0 1969 46 86 2 8 6 6 6 Sere 10969106 79 en 6 e ia Figure 5 4 A layer of atoms a configuration of KCN the disordered phase atoms are purple are black and N are blue The bonds are shown 5 5 Example of using Bond valence s
84. 000 00 0 4766961 00 0 1046322 02 0 9500000 00 0 4731495 00 0 1022877 02 0 9700000 00 0 4702018 00 0 9821923E 03 The lines beginning with the are treated as comments the third comment line is important because it contains the start and end point numbers that are read 4 13 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 lineshape functions obtained from the GSAS program and adjusts the configuration to match the intensities of the Bragg peaks 4 13 1 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 The gt SUPERCELL line within the BRAGG keyword block 80 154 1939 RMCProfile Manual v6 5 2 4 13 BRAGG SCATTERING contains the three integers Nx Ny Nz When we now consider the Miller indices these refer to the fundamental unit 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 13 1a optional hk1 fi
85. 1 0 8This feature has not been used by the current author but by all means try it 57 154 RMCProfile Manual v6 5 2 4 5 USING THE BRAGG PROFILE The spin configuration file like the standard configuration file is updated during the course of the refinement so if you wish to keep track of your starting configuration we suggest you keep a copy of this file separate 4 4 3 Generated files RMCProfile produces three new files when refining a magnetic structure These mag stem name his mag stem name ff and mag stem name braggff The his file performs much the same function as the equivalent histogram file that accompanies the main configuration file The braggff file lists the magnetic form factors for each atom type over the correct Q range for the Bragg data set while the ff file lists the magnetic form factors in a suitable format for the other data sets These will likely play little role in any analysis performed the final spin configuration and the fits to data will be of more use As outlined in Section 2 10 4 the program ATOMEYE can be used to help view the refined structure PYMOL can also be of use 4 5 Using the Bragg profile When the Bragg option is specified RMCProfile extracts the necessary information about back ground and lineshape functions from a GSAS refinement You can of course choose a different Rietveld package for your refinements but in this case you will need to put it in GSAS format at the en
86. 1 248 HexceProNN o s Pbi gAp v HExcEPTONN O S 109 500 1 248 CcsesaLkaNE SesELENIUM CSP3ALKANE 94 800 8 114 Cocsp3aLKANE S SELENIUM HEXCEPTONN O S 94 500 5 368 95 050 8 114 l ereLLURIUM HEXCEPTONN O S 94 600 5 368 Cosp3aLkane Nn c PYR DELOCLZD CcsP2ALKENE 109 000 8 988 CospsaLkane Nn c PYR DELOCLZD Nn c PYR DELOCLZD 106 500 8 613 CcsPsaLkaNE NN c PvR bELOCLzD N NOAZOXY LOCAL 99 100 7 115 CosPeaLkENE NN c PvR pELOCLZD CCSP2ALKENE 112 600 14 980 Cosp2aLkeNe Nn c PYR DELOCLZD HNHAMINE IMINE 109 800 8 364 Cosp2aLkeNe Nn c PYR DELOCLZD Nn c PYR DELOCLZD 107 500 16 228 Ccosp2atkene Nn c PYR DELOCLZD Nsp2PYRROLE 115 000 5 368 HNHAMINE IMINE NN c PYR DELOCLZD Nn c pYR DELocLzp 106 400 11 235 Cosp3aLKANE Ccsp2cYCLOPROPENE CCYCLOPROPANE 117 200 5 617 Cosp2aLKENE Ccsp2cYCLOPROPENE CCYCLOPROPANE 137 000 6 866 HExCEPTONN O S Ccsp2cYCLOPROPENE CCYCLOPROPANE 146 000 4 494 HExcEPTONN O S Ccsp2cYCLOPROPENE CCSP2CYCLOPROPENE 146 000 4 494 Ccosp3aLkane NnspsamMonium CcsPsALKANE 107 114 8 976 CcospsaLkane NnspsammoniuM Hammonium 105 949 6 504 CcospsaLkane NnspsAMMONIUM OAMINEOXIDEOXYGEN 109 700 11 048 Hammonium Nnsp3amMoniuM Hammonium 106 367 7 602 CospsaLkane Nnsp2pyRROLE CcsP2ALKENE 120 500 6 117 Cosp2aLkeNne Nnsp2PyRROLE CcsP2ALKEN
87. 116 900 0 999 Cosp3aLKANE CKETONIUMCARBON OKETONIUMOXYGEN 113 500 13 607 5 0 5 124 500 4 993 3 111 700 2 746 CosPsALKANE N NIMINE LOCALZD CCSP2ALKENE 109 600 8 988 CosPsaLkaNE OoH 0 c cARBOXYL CCSP2CARBONYL 112 800 15 604 CocsPecanBoNvL OonH o c canBOxvL CcsP2CARBONYL 106 800 9 612 CocsPecanBoNvL OoH o cicanBoxvL HcooHcARBOXYL 107 700 8 613 CocsPecanBoNvL OoH o cicaRBOxvL CosPsCYCLOBUTANE 110 800 15 604 180 000 8 738 HNHAMINE IMINE NN N azo LocaL Nn n azo LocaL 106 200 11 235 Cosp2aLkene N noHoxime Oosp2FURAN 107 973 18 725 CosPsaLkaNE NN AzOXY LOCAL N NOAZOXY LOCAL 105 200 14 980 HuuaMINE IMINE NN AzOXY LOCAL N NOAZOXY LOCAL 101 500 14 356 CosPsaLkaNE NN IMMINIUM CCSPSALKANE 117 500 11 235 141 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS CCSP2ALKENE 124 000 5 617 116 700 9 362 CosPzaL kENE NN IMMINIUMHNHAMINE IMINE 119 400 5 617 CosPsaLkaNE NN 4 PYRIDINIUM 119 000 9 987 CosPeaLkENE NN 4 PYRIDINIUM CCSP2ALKENE 120 000 11 235 CosPeaLkENE NN 4 PYRIDINIUM CH NHAMINE IMINE 109 800 9 36
88. 2 8 126 000 4 993 Ccsp3aLkane CPcrerrocenec CPcrerrocenec 126 000 5 867 2 119 100 15 604 Cosp2aLKENE N NoAxoxY DELOC OAMmINEOXIDEOXYGEN 121 700 21 596 Cospeatkene N noaxoxy DELoc Nn azoxy DELOc 114 000 14 356 OamineoxiDEoxYGeN N noaxoxy DELoc Nn azoxy DELOC 136 000 23 469 CosPeaLkENE NN Azoxv pELOC N NOAXOXY DELOC 102 000 9 987 gt gt NOHHYDROXYAMINE 107 500 13 732 HoHALCOHOL O gt NOHHYDROXYAMINE N 5 104 000 11 547 Cosp3aLkane N gt gt NOHHYDROXYAMINE CCSP3ALKANE 98 500 5 742 CospaakaNe N gt NOHHYDROXYAMINE HNHAMINE IMINE 104 500 8 738 gt NOHHYDROXYAMINE O gt NOHHYDROXYAMINE 102 500 15 916 NOHHYDROXYAMINE HNHAMINE IMINE 103 000 9 737 101 500 9 050 OocsPecanBoNvL Oo ANuYpRIDE LOCL CCSP2CARBONYL 110 000 10 361 106 980 13 732 Cosp3aLkane NnspsHYDRAZINE HNHAMINE IMINE 102 350 8 738 CosPaaLkaNE NNsPauvbRAzINE NNsPSHYDRAZINE 102 470 9 987 HNHAMINE IMINE NNsp3HYDRAZINE HNHAMINE IMINE 102 900 8 114 HNHAMINE IMINE NnspsHy
89. 2 jeu pue esiwdejs au ejy Indjno TWX ue ped Jaye eui 8 2 lt 4 433 lt lt 1 1 2 gt 5 96691 85795851 6 lt 5 5 u squrod e9S T1907E9v06L9v CV V lt uSse T O p XO4d y US UCD ejepejeu 2 65536896899 90L9L96v98 1IZ 2 77 962S81Lv8981L 8 2 0 lt 9eez xdg edArleaep 99 4 278 gt lt gt 2 3 uorsue lt uzsqutod lt gt 7 6926562 895275 lt 46 5 gt 0989966866677 lt 485 lt 20 2 1 2 lt gt lt lt 3 3 lt gt 36 1 3 5 1
90. 2 C Alkane Csp3 7 NGuanidinium C Guanidinium 120 400 9 113 Clkane Csp3 NGuanidinium I Guanidinium 122 400 2 372 144 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS Cauanidinium NGuanidinium H Guanidinium 120 500 7 240 Hauanidinium NGuanidinium H Guanidinium 123 000 5 118 124 000 5 368 118 000 4 494 Catkene His TrpC C Npyrrole Hpyrrote 118 000 4 494 Calkene His TrpC C N midazolium C Imidazolium NC N 115 000 5 368 Calkene His TrpC C NImidazolium H imidazolium 110 000 6 242 Cimidazolium NC N N imidazolium H imidazolium 110 000 6 242 Catkane Csp3 Oaicohol Phenol Halcohol Phenol 106 800 9 362 109 000 4 494 Hatcohol Phenol Oalcohol PhenolHaicohol Phenol 105 000 7 864 C Alkane Csp3 S Sulfide C alkane Csp3 95 900 10 486 C Alkane Csp3 9 Sulfide 9 Sulfide 102 000 12 483 Catkane Csp3 SSultide H Thiol SH 96 000 8 114 145 154 RMCProfile Manual v6 5 2 APPENDIX C BOND VALENCE PARAMETERS Appendix C Bond valence parameters 3 1 Values for bond valence sum calculation The values in the table below are taken from Brese and O Keefe Acta Cryst 47 192 197 1991 Values for anions other than O F and Cl can be found in that paper along with a discussion of how they were determined T
91. 2 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 parameters note that 5 summon help or summon h will provide a summary of the required parameters 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 in the user s directory The first parameter i e the one following
92. 292999 1 12E 02 21 310051 2 57E 02 21 327099 2 65E 02 81 154 RMCProfile Manual v6 5 2 4 14 RMCPROFILE VERSION 3 FILES 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 inst 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 13 26 back As in Rietveld refinement the backgound is modelled using Chebychev polynomails This file con tains the number of polynomials on the first line followed by the coefficients one per line 4 13 2c inst file This file is extracted from the GSAS files It has the form 4 1456 13 0 53 02 17 98 0 000000 00 0 381440 00 0 322500 02 0 532200 02 0 000000 00 0 204539 03 0 000000 00 0 000000 00 0 126026 02 0 000000 00 0 000000 00 0 000000 00 The first line contains the number of detector banks the instrument Then follows 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 13 3 Generated files RMCProfile automatically generates two files namely a amp file and one called hk1s These are used for subsequent restarts and the user need not be concerned
93. 2aLKeNe Ccsp3aLKANE NNn c PYR DELOCLZD 110 510 4 744 Ccsp2atkeNe Ccsp3aLKANeE Nnsp3aMMONIUM 110 740 13 045 CosPeaLkENE CcsPsaLkaNE 7 N NOAZOXY LOCAL 110 510 4 744 109 470 5 867 5 109 490 6 741 0 109 500 8 738 110 740 13 045 CcspacarBonyL CcspsaLKANe Nnsp2 109 500 10 611 CcspecarBonyL Ccsp3aLKANE F FLUORIDE 109 200 9 487 CcspecarsonyL Ccsp3aLkANE CIcHLORIDE 109 800 8 114 CcspecarsonyL Ccsp3aLKANE BIBROMIDE 109 100 9 362 CcspecarsonyL Ccsp3aLkANE lopIDE 108 900 7 490 CcspecarBonyL Ccsp3ALKANE SS SULFIDE 107 800 5 243 CcspacarBonyL CcspsALKANE S gt S SULFONIUM 107 800 5 243 CcspacarBonyL CcspsaLKANe DDEUTERIUM 109 490 6 741 CcspacarBonyL CcspsaLKANE NnsP3aMMONIUM 110 740 13 045 CosraLkvNE CcsPsALKANE CCSPALKYNE 109 470 5 867 5 109 390 8 489 109 000 11 235 5 110 700 15 979 Ccspatkyne Ccsp3aLkKANE OOH 0 C CARBOXYL 107 500 9 987 5 0 5 107 600 6 866
94. 3 H ACID 1 21 4 703 121 4 703 CospecarRBonyL Oo cx HALIDE 1 20 5 591 lt 121 4 627 1 20 5 087 121 4319 1 20 4 607 lt 1 21 5 183 Ccsp2caRBONYL Oo ANHYDRIDE LOCL 1 41 2 064 1 21 7 319 1 16 8 317 1 31 5 375 1 08 2 865 HexCEPTONN O S S gt S SULFONIUM 1 35 1 824 HexXCEPTONN O S S gt S OSULFOXIDE 1 37 1 521 HExCEPTONN O S S gt SO2SULFONE 1 35 1 824 123 154 RMCProfile Manual v6 5 2 2 1 BOND STRETCHING TERMS HexcEPTONN O S SIsILANE 1 48 1 272 HexcEPTONN O S CCYCLOPROPANE 1 09 2 438 HexcEPTONN O S P gt PPHOSPHINE 1 42 1 471 0 87 C RADICAL 1 10 2 505 HexcEPTONN O S GEGERMANIUM 1 53 1 224 8 1 70 1 070 0 5 1 77 0 909 HeXCEPTONN O S SESELENIUM 1 47 1 521 0 5 T TELLURIUM 1 67 1 368 HexCEPTONN O S CcSP2CYCLOPROPENE 1 07 2 208 HexcEPTONN o s CBENZENE LOCALIZED 1 10 2 472 0 87 CcsPscYCLOBUTANE 1 11 2 275
95. 3 35 x x y 3x y 4 4 50 67 154 RMCProfile Manual v6 5 2 4 8 USING BOND VALENCE SUM These quantities are averaged over each bond for any given bond type and also averaged over steps The resultant averages namely Y m and Y m are printed in a file with name lt file gt y1m 4 7 8 Generation of Kubic harmonic function averages If rmcprofile deduces that the RMC configuration is likely to be of a cubic lattice type it will cal culate the averages of the Kubic harmonics 0 of the appropriate symmetries for the molecular bonds where represents the polar coordinates describing the orientation of a bond The harmonics calculated are the following where Q x y 24 and 2 222 1 4 51 50 3 4 52 5 9 5 18 2 4628 210 17 4 53 Kg Q ao 581 6502 2085 940 33 4 54 A 155 2 71 0605 187Q 3190 2640 85 4 55 The value the Kubic harmonics is that bond orientation distribution function for molecule lo cated at a site of octahedral symmetry point groups Op or m3m can be expressed as an expansion in these functions 1 a c K Q 4 56 Tg where only even terms are allowed by symmetry and c 4 57 As with the spherical harmonic quantities above values of the Kubic harmonics are averaged over each bond for any given bond ty
96. 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 2 have added a number of new subroutines to make this work 151 154 RMCProfile Manual v6 5 2 3 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 procedure working 4 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 5 think that the code still generates file when you don t want one so need to look at this another tweak 6 doubt that restarting from his6f works because need to copy some fixes from the rmc 6f code would like to see that the xmc6 stuff works first another tweak 7 would like to put the experimental
97. 4 RMCProfile Manual v6 5 2 4 10 POLYHEDRAL RESTRAINTS 4 10 10 The NaNO restraint 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 To use this restraint option 10 needs to be specified in the dat file and poly and on files supplied The poly file contains a title line which is ignored and the next line must contain the ideal 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 each oxygen atom both of these files should be generated using the neighbour list program supplied with RMCProfile and described in section 6 1 4 10 11 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 dat file and 1 cn and files supplied The poly contains a title line which is ignored and the next line must contain the ideal bond distance to be used and the w
98. 5 154 RMCProfile Manual v6 5 2 4 15 UPGRADE TO V6 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 14 2 The c g file The file contains the information about the supercell of atoms RMCProfile will use to fit the data This file together with the aat 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 overall format is fixed so the easiest way to produce this file is to use the crystal program supplied with RMCProfile 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 sys
99. 51 2 304 Catkane Csp3 C carboxy 1 51 2 304 Coheed 150 3 024 Catkane Csp3 Calkene His TrpC C 1 50 3 024 Calkane Csp3 Namide 1 45 2 501 Calkane Csp3 NAmmonium 1 47 1 896 NGuanidinium 1 45 2 501 141 2 736 Catkane Csp3 S Sulfide 1 80 1 440 Catkane Csp3 HH Hydrogen CH 111 2 275 Camide Namide 1 33 3 216 Camide Oamide 1 23 4 415 1 12 2 097 Ccarboxyr Ocarboxytate 1 25 3 633 1 39 3 148 Cphenyi Calkene His TrpC C 1 48 2 304 1 35 3 840 126 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS 1 35 2 880 110 2 472 Ceuanidinium Neuanidinium 1 32 3 278 Calkene His TrpC C 1 33 3 600 Calkene His TrpC C NPyrrole 1 35 3 840 1 35 3 840 1 10 2 472 Cimidazolium NC N N imidazolium 1 35 3 840 Cimidazolium NC N HH Hydrogen CH 1 10 2 208 Namide Hamide 1 03 3 249 Nammonium Hammonium 1 04 2 928 Nuanidinium Heuanidinium 1 03 3 249 1 05 2 928 Nimidazotium H imidazolium 1 04 2 928 Onicohol Phenor HAlcohol Phenol 0 95 3 662 Ssutide Ssultide 2 02 1 257 Sssuitige Hrhiol SH 1 34 1 857
100. 6 1424 5187 2 867 1425 5188 2 868 1426 5189 2 869 1427 5190 2 870 1428 5191 2 871 1429 5192 2 872 1430 51 93 2 873 1431 5194 2 874 1405 5 8 Example of using magnetism Coming soon 97 154 RMCProfile Manual v6 5 2 5 9 EXAMPLE OF USING EXAFS DATA 5 9 Example of using EXAFS data Coming soon 5 10 Example of using X ray data There is now a tutorial on using X ray data in the tutorials folder included with your RMCProfile download 98 154 Manual v6 5 2 CHAPTER 6 TOOLS FOR DATA PREPARATION AND ANALYSIS Chapter 6 Tools for data preparation and analysis 6 1 Data preparation 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
101. 8 1 68 2 05 1 904 1 811 2 23 1 879 1 759 2 17 Celll 2 151 2 036 2 52 Pulll 2 11 2 2 48 CelV 2 028 1 995 2 41 Rb 2 26 216 2 65 Cf Ill 2 07 1 05 2 45 Re VII 1 97 1 86 2 23 1 632 1 55 2 00 1 791 1 71 2 17 2 23 212 2 62 IV 1 834 174 221 Coll 1 692 1 64 2 01 SIV 1 644 16 2 02 Coll 1 70 1 62 2 05 SVI 1 624 1 56 2 03 Cr Il 173 1 67 2 09 1 973 1 9 2 35 Crill 1 724 1 64 2 08 SbV 1 942 1 8 2 3 1 794 1 74 2 12 1 849 1 76 2 23 Cs 242 2 33 2 79 1 811 1 73 2 22 Cul 1 593 1 60 1 85 Se VI 1 788 1 69 2 16 Cull 1 679 1 60 2 00 Silv 1 624 1 58 2 03 Dy 2 036 1 922 2 41 Sm 2 088 1 977 2 466 Er Ill 2 01 1 906 2 39 1 984 1 925 2 36 Eull 2147 2 04 2 53 SnlV 1 905 1 84 2 28 Eu lll 2 076 1 961 2 455 Srll 2 118 2 019 2 51 Fell 1 734 1 65 2 06 1 92 1 88 2 3 Fell 1 759 1 67 2 09 Tb Ill 2 049 1 936 2 427 147 154 RMCProfile Manual v6 5 2 3 1 VALUES FOR BOND VALENCE SUM CALCULATION Ga Ill 1 73 1 62 2 07 lV 1977 1 87 2 37 2 065 1 05 2 445 1 917 1 82 2 3 1 748 166 2 14 ThiV 2 167 2 07 2 55 0 95 0 92 1 28 Ti lll 1 791 1 723 2 17 1 923 1 85 2 30 1 815 176 2 19 1 90 1 81 2 28 TII 2 172 215 2 56 Hg Il 1 93 1 90 225 2 003 1 88 2 32 2 023 1 908 2 401 Tm 2 1 842 2 38 IV 2 00 1 90 2 38 UIV 2 112 2 034 2 48
102. 80 000 4 993 180 000 5 867 180 000 3 121 Nnsp CcspatkyNe CBENZENE LOCALIZED 180 000 1 598 CcspaatKkane Oco H c_o c o o CcsP3ALKANE 107 200 10 236 CospaatKane Oco H c_o c o o CcsP2ALKENE 108 500 9 612 CospsatkaNE Oco H c o c o o C csp2caRBONYL 112 800 15 604 0 103 300 13 207 0 5 117 100 7 864 0 106 800 9 362 CcspsaLkane Oco H c 0 c 0 0 P gt PPHOSPHINE 116 000 9 612 0 108 900 8 613 0 0 0 gt 119 600 17 227 109 000 4 494 gt 118 000 9 987 Cosp2aLKENE Oco H c o c o O HHoENOL PHENOL 108 000 4 369 CcspecarsonyL Oco H c o c o o Ccsp2caRBONYL 106 800 9 612 107 700 8 613 0 0 110 800 15 604
103. 988 109 700 8 613 104 800 8 676 Ss suLFiDE CcsP3ALKANE SS SULFIDE 110 000 5 243 Sisitane CcspsaLkANE SISILANE 109 500 4 369 CcycLopROPANE CCSP3ALKANE CCYCLOPROPANE 112 600 5 992 CcvcLoPRoPANE CcsPsaLkaNE NN C PYR DELOCLZD 110 200 4 744 CocvcLoPRoPANE CcsPsALKaANE N NOAZOXY LOCAL 110 200 4 744 Dpeuterium Ccsp3aLKANE DDEUTERIUM 107 600 6 866 Nu c PvR pELocLzb CcsPsALKANE NN C PYR DELOCLZD 109 000 11 859 109 500 7 989 CaeNzENE LOCALIZED CCsP3ALKANE CBENZENE LOCALIZED 113 200 5 617 CcsP2cvctoBUTENE CcsPsALkANE CCsP2CYCLOBUTENE 113 200 5 617 2 117 000 6 741 2 2 122 300 5 867 2 117 000 6 242 CCSPALKYNE 116 600 5 867 0 3 117 500 6 117 0 120 000 6 242 CcsPaaLkaNE CcsPeALKENE 120 000 4 993 117 500 6 117 Cosp3aLKaNe Ccsp2aLKENE Nn c PYR DELOCLZD 115 100 8 988
104. CProfile because we 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 It can then be run on the command line by typing atomeye bat lt lt atomeye file gt gt where atomeye file is replaced by the con figuration converted by the program rmc_to_atomeye i e rmcsf 6_190k eyecfg 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 6 3 CML based analysis tools With the use of the CML keyword RMCProfile will generate an XML file containing a rich set of output data in the Chemical Markup Language CML format as described previously The power of XML is obtained from tools that can process XML documents Here we describe two tools that exploit the use of CML to the RMC user s advantage 6 3 1 ccViz tool ccViz is a python program written by Toby White that will produce and information centric report in XTHML format e a report that can be read us
105. Ccsp3ALKANE NN PYRIDINIUM 108 640 12 234 CcsesaLkaNE CcsPsaLkaNE NNsP3HYDRAZINE 109 140 9 737 gt 109 500 6 242 9 gt SO2SULFONAMIDE 108 154 15 454 109 500 10 361 113 200 5 617 2 2 109 470 5 867 CcsreaLkENE CcsPsALKANE CCSPALKYNE 109 470 7 115 2 0 3 109 500 6 866 2 0 0 0 107 000 8 738 110 740 13 045 gt 109 800 6 242 128 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS 129 154 Cosp2aLkENE CcsPsALKANE F FLUORIDE 109 000 9 487 Cosp2aLkeNe CcsPsALKANE ClIcHLoRIDE 109 500 8 114 Cosp2aLkeNe CcsPsALKANE lioDIDE 109 300 8 676 CosreaLkENE CcsPsALKANE Ss sULFIDE 107 800 8 114 CcsreaLkeNE CcsPsALKANE S 8 SULFONIUM 107 800 5 243 CcsreaLkeNE CcsPsaLkaNE SlsiLANE 109 500 6 242 112 400 5 617 Ccsp2atkeNe CcspsaLKANe DDEUTERIUM 109 500 6 866 Cosp
106. DRAZINE NNsp3HYDRAZINE 104 580 10 860 gt p oPHOSPHATE CCSP3ALKANE 109 200 4 993 gt 5 105 500 6 242 Cocsp3aLKANE P gt p oPHOSPHATE Oco H C_O C O O 107 200 4 494 CcsPsaLkANE P gt 117 500 9 987 gt 104 700 6 866 0 8 gt 0 5 104 500 5 243 8 gt 0 0 0 101 200 7 989 8 gt 0 116 700 10 361 0 87 gt 102 000 8 738 gt 102 900 13 732 0 0 gt 0 117 200 11 734 gt 116 200 14 730 gt 103 500 11 235 142 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS gt S02SULFONAMIDE O0 CCARBONYL 108 728 9 325 5 gt so SULFONAMIDE NNSP3SULFONAMIDE 102 092 7 240 HEXCEPTONN 0 879 80280
107. Definitions were taken from http en wikipedia org wiki Table_of_spherical_harmonics but slightly re arranged in a logical order Real spherical harmonics with 1 1 gt 4 27 0 M 4 28 gt 02 429 Real spherical harmonics with 2 yal ifs 5 e 4 30 1 2 4 31 yo 0 Y gt 24 4 32 V1 ve 5 ae 4 33 ie MAN IE x y B 02 4 34 Real spherical harmonics with 3 ay ys 3 3 24052 4 35 r 1 T 1 105 xyz ineo 6 OL rA n 66 154 RMCProfile Manual v6 5 2 4 7 USING POTENTIALS Ae 4 37 4 38 ya 1 2t Xy 4 39 2 2 1 2 2 4 40 1 vt 1 85 6 9 xd idus gb ax ye niei 5 Ya 2 4 42 _ ya 3 35 3 2 ySyz 72 1 E 4 43 2 i ye 4 44 0 71477 aM r 3 5 yz 722 CI LLL IET 8 1 352 30271 37 4 0 Y2 4 46 1 1 v1 3 5 7z 4 47 nr 205 T 1 3V 2 Poo o5 EE x 2 722 r ya 2 Yee 72 3 E 4 48 fva ya 3 35 x 1 E 4 49 17
108. E N_NOHOXIME LKENE NN IMMINIUM LKENE NN 4 PYRIDINIUM LKENE N NOAXOXY DELOC NusPa CcsP2ALKENE CYCLOPROPANE 2 2 2 Fr_uorIDE Ccsp2aLKENE C C OKETENE ClcuLonipe CcsPezaLkeNE ClcuLonipE gt 2 gt liopipe7CcsPza keNE OosPzFURAN CcsP2ALKENE 915 Dpeuterium Ccsp2aLkENE DDEUTERIUM Nn c PYR DELOCLZD Ccsp2aLkENE Nn c PYR DELOCLZD Nn c PYR DELOCLZD Ccsp2aLKENE NNsp2PYRROLE Sssp2THIOPHENE C cSP2ALKENE OSSP2THIOPHENE CospsaLkKANE Ccsp2ca CospsaLkKANE Ccsp2ca Cosp3aLKaNnE Ccsp2ca 2 2 2 2 5 RBONYL Ccsp2ALKENE RBONYL C csp2cARBONYL RBONYL H 0 5 RBONYL Oo cCARBONYL RBONYL Nwsp2 2 2 BOND BENDING TERMS 119 000 119 000 120 000 110 000 108 000 120 100 116 500 116 000 120 000 120 000 121 700 114 000
109. E 124 000 5 368 Ccsp2atkeNe Nnsp2PYRROLE HNHAMINE IMINE 118 500 6 117 Ccsp2atkene Nnsp2pYRROLE NN c PYR DELOCLZD 124 000 5 368 HnHAMINE IMINE NINsp2PYRROLE NN c PYR DELOCLZD 116 000 6 117 Ccspaatkane Oosp2FuRAN CCSP2ALKENE 109 100 12 483 CcspaatkaNe Oosp2ruRAN N NOHOXIME 110 510 11 235 5 2 112 000 11 859 2 2 107 000 10 611 110 850 11 235 HuoeNou PHENOL OosPezrURAN N NOHOXIME 101 884 12 483 Cosp2aLkENE Sssp2THIOPHENE CCSP2ALKENE 98 500 8 489 Cosp2aLkENE Sssp2THIOPHENE HsHTHIOL 94 000 9 362 139 154 RMCProfile Manual v6 5 2 CocsPaaLkaNE N NOAZOXY LOCAL CosPaaLkaNE N NOAZOXY LOCAL CosPaaLkaNE N NOAZOXY LOCAL CosPaaLkaNE N NOAZOXY LOCAL CosPeALKENE N NOAZOXY LOCAL CosPeALKENE N NOAZOXY LOCAL Oo ccARBONYL N C PYR DELOCLZD OAMINEOXIDEOXYGEN NN azOXY LOCAL CSP2ALKEN E OAMINEOXIDEOXYGEN Oo ccanBoNvL N NoAzOXY LOCAL NN C PYR DELOCLZD HNHAMINE IMINE N NOAZOXY LOCAL OXAMINEOXIDEOXYGEN HNHAMINE IMINE N NOAZOXY LOCAL NN AZOXY LOCAL OawiNEOXIDEOXYGEN N NoAzOXY LOCAL N N AZOXY LOCAL Oo ccangoNv Nurrgo Oo ccARBONYL Oo c
110. ELLING ATOMIC SITE DISORDER THROUGH ATOM SWAP MOVES The implementation of bond valence sums as soft chemical constraint RMCProfile is dis cussed further in 11 2 7 Modelling atomic site disorder through atom swap moves Many materials contain some degree of chemical disorder For example materials in the perovskite solid solution series CaTiO3 SrTiO3 may have disorder of the Ca and Sr atoms over the 12 coordinated sites or for some compositions there may be some degree of long range order eg at a 50 50 composition there is the possibility for these cations to order in a NaCl type ordering pattern Moreover regardless of the state of long range order there may be some degree of short range order This is exactly the sort of problem that RMC should be capable of tacking but in crystalline materials it is virtually impossible for atoms to swap positions simply through the normal small step movements that are used in the method Instead RMC allows moves in which two atoms selected from a specified list of atom types swap positions The intensities of peaks in the pair distribution function should be sensitive to the site occupancies given that the numbers of neighbours in any specific peak in the pair distribution function is determined by the crystal structure The specific example of the CaTiO3 SrTiOg is described in 10 2 8 Coordination Constraints Coordination constraints are still a functioning part of the RMCProfile code
111. Figure 5 2 The PDF D r for KCN comparing experimental data black line and the fitted function from the RMC model red line 2 The data file was produced by the STOG program The fitted function is shown in Figure 5 2 The very sharp first peak represents the bond and is so sharp because this is a strong covalent bond of high stretching frequency and hence low amplitude for stretching motions Note that the D r function does not diverge at low r This is a good sign a peak at very low r is a characteristic sign of inadequate data correction 5 3 Example of using the Bragg profile 5 31 Bragg profile files Our example here will be KCN at 50 K where the orientations of the CN molecular anions are ordered The file containing the Bragg profile data has the form 1781 2 12 38600 133 5340 Time I obs KCN_50K_LONG 5 003600 3 6351800 02 5 007605 3 9751101 02 5 011610 4 3346100 02 5 015615 4 7388699 02 5 023650 5 5795401 02 5 027670 5 9385199 02 5 031691 6 1015900 02 5 035715 6 0725201 02 5 039745 5 9345201 02 5 043775 5 6898199 02 91 154 Manual v6 5 2 5 4 EXAMPLE OF USING POTENTIALS where the file is simply a list of flight time and intensity data The first number given is the number of points the second is the bank number see next file the third is the scale factor given by the GSAS Rietveld refinement and the fourth is the unit cell volume which is not used The Bragg
112. ME GEM12285 sq gt DATA_TYPE F Q gt FIT_TYPE F Q gt START_POINT 1 gt END_POINT 2000 gt CONSTANT_OFFSET 0 0000 gt WEIGHT 0 005 gt NO_FITTED_OFFSET gt NO_FITTED_SCALE gt STOG gt CONVOLVE The key points from this example are 1 We are using the F Q i Q functions both are equivalent for both the input data format and for the RMC analysis In this format the errors are more or less equal for each point 2 The data file was produced by the STOG program 3 We have instructed RMCProt file to convolve the experimental data with the Fourier trans form of a box function with width equal to the maximum distance in the PDF generated by RMCProfile from the atomic configuration The fitted function is shown in Figure 5 1 The effect of the convolution with the box function is shown by the strong oscillations in the function In practice the data extend to much higher values of Q than shown in the plot but showing the high Q data would have squeezed the higher intensity data into the far left hand side of the plot 89 154 RMCProfile Manual v6 5 2 5 2 USING PDF DATA 5 2 Example of using pair distribution function data 5 2 1 Neutron PDF data file We consider here the same RMC study of KCN in its disordered phase The PDF data file was obtained by Fourier transform of the merged data set and has the form File pair distribution function file Generated using stog version
113. NNsp3 LOBUTANE NNsp2 95 SULFIDE LOBUTANE C CYCLOPROPANE LOBUTANE G GERMANIUM LOBUTANE CCSP3CYCLOBUTANE 2 2 BOND BENDING TERMS 120 400 114 000 117 000 118 000 117 300 117 000 125 000 108 000 106 000 124 200 115 900 116 100 127 700 114 500 122 300 121 700 121 200 120 000 123 000 109 500 110 100 109 300 110 700 0 000 109 500 110 300 109 300 109 490 109 500 107 600 108 700 109 300 111 000 111 500 110 000 112 000 110 200 110 100 110 000 7 115 4 744 11 485 12 109 15 604 21 596 4 744 9 737 11 422 22 720 12 483 17 726 12 483 12 733 5 867 9 487 5 368 6 117 7 490 8 364 7 365 9 612 12 858 8 364 8 364 6 242 9 612 6 741 8 114 6 866 5 617 10 236 9 487 9 238 8 489 4 494 4 993 7 365 6 117 140 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS 5 CcsPscvcLoBUTANE C C OCYCLOBUTANONE 110 490 7 864 0 57 CcsPscvcLoBuTANE OoH 0 c CARBOXYL 108 700 5 617 2 110 500 6 991 109 100 13 482 Nnsp3 Ccsp3cYcLOBUTANE Ccsp3CYCLOBUTANE 109 470 9 737 Sisitane CcspscYCLOBUTANE C cSP3CYCLOBUTANE 111 000 5 992 Gegermanium Ccsp3cYCLOBUTANE Ccsp3CYCLOBUTANE 11
114. Nn c PYR DELOCLZD N noazoxy LOcaL 1 26 5 145 CcspacycLopROPENE CcsP2CYCLOPROPENE 1 30 4 607 NusP3AMMONIUM NNSPSAMMONIUM 1 25 5 145 NusP3AMMONIUM NNsP2PYRROLE 1 28 5 279 NusP3AMMONIUM HAMMONIUM 1 05 2 947 NusP3AMMONIUM AMINEOXIDEOXYGEN 1 36 2 208 2 0 96 3 456 1 40 2 073 125 154 RMCProfile Manual v6 5 2 2 1 BOND STRETCHING TERMS SgspeTHIOPHENEHsHTHIOL 1 34 1 867 N NoAZOXY LOCAL OAMINEOXIDEOXYGEN 1 27 4 223 N NoAzOxv LOCAL NN AZOXY LOCAL 1 26 3 408 CsaENzENE LOCALIZED CBENZENE LOCALIZED 1 39 3 148 CcspacYcLOBUTANE CCSP3CYCLOBUTANE 1 50 2 155 CcspecYcLOBUTENE CcsP2cYCLOBUTENE 1 33 3 600 1 17 5 039 Cc ocvcLoBUTANONE OO cN AMIDE 1 21 3 360 1 28 4319 1 25 4 080 N_noaxoxy DELoc Nn azoxy DELOC 1 26 4 223 gt 1 41 2 160 NusesHvpRAziNE NNsP3HYDRAZINE 1 55 1 440 1 60 2 736 gt so2suLFONAMIDE Nsp3sULFONAMIDE 1 70 1 893 Table B 2 Bond stretching terms from the protein set parameters Catkane Csp3 C alkane Csp3 1 52 2 155 Catkane Csp3 C amide 1
115. Profile is instructed to include magnetic scattering by inserting the appropriate text into the version 6 dat file An example is shown below MAGNETISM gt MAGNETISM FILE STEM fe3o4 spin gt ATOMS 2 gt FORM_FACTOR 1 0 3972 13 2443 0 6295 4 9034 0 0314 0 3496 0 0044 gt FORM_FACTOR 2 0 3972 13 2443 0 6295 4 9034 0 0314 0 3496 0 0044 gt 5 4 625 4 130 gt SPIN MOVEMENT 0 05 gt MOVE RATE 0 5 gt VARY SPIN MOVE RATE Here the MAGNETISM major keyword indicates the beginning of the magnetism section As with other sections the order of the following subordinate keywords is arbitrary and left to the whim of the user The keywords available are described above in Section 4 1 4 but we shall discuss them here as well to avoid excessive scrolling Taking the keywords in the order listed above we start with gt MAGNETISM FILE STEM fe3o4 spin This instructs the program to look for a file called fe304 spin cfg containing the spin configuration on which we shall say more later and to name any associated magnetism output files in that way The gt MAGNETIC ATOMS 2 line tells Thank you to Callum Young for writing this section 56 154 RMCProfile Manual v6 5 2 4 4 USING MAGNETISM the program that there are two magnetic atom types in the structure It is assumed that thes
116. RMCProfile User Manual Code version 6 5 2 Matt Tucker Martin Dove Andrew Goodwin David Keen Helen Playford June 27 2014 RMCProfile Manual v6 5 2 Contents 1 Introduction 1 14 We know you don t read manuals 1 2 What and why of RMC 1 3 RMCProfile introduction 2 Capabilities 21 Fitting neutron and X ray total scattering data 2 2 Fitting PDF data 2 3 Fitting the Bragg profile 2 4 Distance window constraints 2 5 Interatomic potentials 2 6 Bond valence constraints 2 7 Modelling atomic site disorder through atom swap moves 2 8 Coordination Constraints 2 9 Polyhedral restraints 2 10 Magnetic structure modelling 2 11 Fitting EXAFS data 2 12 Producing starting configurations 2 13 XML output files 3 Installing and Running RMCProfile 3 1 Installation 3 2 Setting up the files for an RMCProfile calculation 3 3 Running RMCProfile 3 4 Output files 4 Input Files 4 1 RMCProfile main data file 4 2 Neutron and X ray coefficients 4 3 Using experimental data 44 Using magnetism 4 5 Using the Bragg profile 4 6 Using EXAFS data 4 7 Using potentials 4 8 Using Bond valence sum 4 9 Using constraints and restraints 4 10 Polyhedral restraints 4 11 RMC Version 6 format configuration files 4 12 Experimental data files 4 13 Bragg scattering 4 14 RMCProfile version 3 files 4 15 Upgrade to v6 CONTENTS gt 10 11 12 13 13 14 14 14 15 23 23 24 28 28 29 30 31 33 33 51 51 56
117. RMS Cosp3aLkaNE NN 4 IMMINIUM 1 47 3 081 CocsPsALKANE NN PYRIDINIUM 148 2 640 1 51 3 024 gt 1 37 2 808 CcspsaLkane N gt NOHHYDROXYAMINE 1 41 2 304 1 5 1 44 1 824 gt 1 80 1 584 CcsP3ALKANE S gt SO SULFONAMIDE 1 78 1 490 CcsPsaLkaNE NNSP3SULFONAMIDE 145 2 138 1 42 2 112 Cosp2aLkENE CcsP2ALKENE 1 33 3 600 Cosp2aLkENE CcsP2cARBONYL 1 35 4 080 Cosp2aLkENE CCSPALKYNE 1 31 5 375 0 5 1 10 2 472 0 1 35 2 880 1 37 3 033 2 1 41 2 860 1 35 2 640 CcspzaLkene ClcHLORIDE 1 73 1 344 1 89 1 200 2 08 1 190 gt 80280 1 77 1 344 Ccsp2aLkENE SIsILANE 1 85 1 440 CcsreaLkENE CcvcLoPROPANE 1 46 2 736 CcsPeALkENE P gt PPHOSPHINE 1 83 1 397 Ccsp2aLkENE B gt BTRIGONAL 1 55 1 661 Ccosp2aLkKENE GEGERMANIUM 1 94 1 718 Cosp2aLkENE DDEUTERIUM 1 10 2 472 2 PYR DELOCLZD 1 27 4 319 2 1 34 4 607
118. RSION Requires labels for the atoms in the configura tion file This keyword is not required when Ver sion 6 configuration files are being used Requires an integer which identifies the number of average coordination constraints to be used Is followed by a subordinate keyword to define the parameters 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 data Introduces a block of subordinate keywords which define the parameters used for the bond valence constraint f this keyword is not present the program will search for a bvs file and if neither is present the BVS constraint will not be used 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 6 3 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
119. TWX ue ped 45 BY 2 lt 1 2 gt 2 lt 0 gt lt gt u Suorqoung lt gt 2 lt lt 36 1193 lt gt gt gt lt 1 05 gt 2 2000000002192 3 83 lt adequnwN eueu dequnu e rgjoado 8 8211 882 lt 53 53 lt Setoeds 5 seroeds jo 5 0 OD lt 5 u lt SedAq wo jy eweu buy lt Ssetoeds agequnyN eueu seroeds uM 00 223U943uo2
120. Time between configuration saves Multiplication of three unit cell edges to create configuration Metadata item on sample temperature Time limit set for job Relative weights for each dataset Use numbers 2 3 etc for subsequent datasets Data type Array Array Scalar Scalar Array Text Text Array Array Array Array Array Array Array Scalar Text Text Matrix Array Array Array Array Array Scalar Scalar Scalar Scalar Scalar Scalar Array Scalar Array Array Array Text Text Scalar Array Array Array Array Array Array Array Text Scalar Array Text Scalar Array 111 154 RMCProfile Manual v6 5 2 6 3 CML BASED ANALYSIS TOOLS type scalar xpath cml parameterList cml parameter GdictRef 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 species in the example XML file shown in Figure 2 8 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 li
121. ad 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 successive 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 m
122. aint option 2 needs to be specified in the dat and poly cio and ot i files supplied The 1 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 t io 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 both of these files should be generated using the neighbour list program supplied with RMCProfile and described in section 6 1 4 10 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 needs to be specified in the dat file and poly and files supplied The 1 file contains a title line which is ignored and the next line must contain the ideal C D 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 contains a list of deuterium neighbours around each carbon atom and the file contains a list of the carbon neighbours 71 154 RMCProfile Manual v6 5 2 4 10 POLYHEDRAL RESTRAINTS around each deuterium atom both of these
123. ange of values of angles around the equilib rium angle 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 gt PLOT 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 the US spelling color will also work 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 2 axis with the choice of units being deg or rad gt STRETCH 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 STRETCH SEARCH Give the range of values of distances around the equi librium distance rg 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 in which case give the units as TEMPERATURE Sample temperature in units of Kelvin or in which case specify the units as or C respectively The default units are
124. ant 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 116 154 RMCProfile Manual v6 5 2 1 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 1 2 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 and Q We write rkl Q and x cos 0 and calculate the orientational average for one vector as 1 2 exp 19 2 f sin 040 cos 0 A 13 1 f 5 E 5 dx 14 _ 8 Om A 15 Thus for all atoms we obtain S Q bjby A 16 jk Y bi Y bjb sin Qrj Qrg A17 j jzk where we separate
125. atch this space In some of the examples above we used a wildcard to specify the XML file ie xm1 so doing if this points to several XML files the result will be 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 6 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 113 154 RMCProfile Manual v6 5 2 APPENDIX A BASIC THEORY OF TOTAL SCATTERING Appendix A Basic theory of total scattering 1 1 Theoretical basics of 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 9 and includes scattering with all possible changes of energy of the radiation It therefore encompasses elastic scattering such as from Bragg peaks 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 p
126. ated 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 20 154 Manual v6 5 2 2 10 MAGNETIC STRUCTURE MODELLING Meanwhile what we really want to do is to see what the newly refined magnetic structure looks like We will 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 2 5 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 TEE gt 2 Figure 2 5 A typical equilibrium configuration as seen 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
127. ature because this discussion ignores the effect of quantum zero point motions in which case it might be necessary to use a higher temperature 60 154 Manual v6 5 2 4 7 USING POTENTIALS 4 7 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 simulation 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 E 3S C Le 1 lt gt 10 Zn 2 36 7 4C 6C 10 C 4 2 4n 2 SC 8 CQ 4 Z2 1 Zn AC Z er 1 20 3 lt snip gt 2 Zn O C 2 X Zane L The structure this is important The Metadata lines are important to link this with the actual simulation but will be ignored by RMCProfile They are their for your benefit so don t delete t
128. btained as the Fourier transform of the scattering data There are a number of approaches to computing this transform If data are collected on an instrument such as GEM at ISIS which is typical of instruments at pulsed spallation sources the scattering data are obtained separately for different banks of detectors The common practice within the liquids and amorphous materials communities is to merge data from all banks to produce an overall scattering function This overall scattering function can then be Fourier transformed quite easily The same practice can be followed for crystalline materials and although we sometimes do this in all honesty it is not a good idea to do so The patterns from the different banks have different resolution functions which can easily be seen when comparing Bragg peaks seen in several banks Usually the Bragg peaks in the detectors with lower scattering angles are broader there is an important cot 0 term in the function describing the resolution Thus merging of data typically means that you slice together data from different banks of detectors rather than adding the data when obtained in different banks Such a approach is really being rather cavalier with the effects of resolution but it is what is commonly done Thus we recommend that resolution be taken into account within the process of converting the total scattering data into the PDF One approach is to use the MCGR method 9 in which a model PDF is adjus
129. by double clicking on the bat file your path should be set for you and you will not have to worry about locating the individual programs They should run from your RMCProfile command prompt window 3 4 Output files RMCP rofile will generate a number of output files These include following the methane example given above methane out contains a lot of summary information and generated data methane xml contains lot of summary information and generated data if you have specified request for CML data methane xhtml contains a nice web page summary of the results of the simulation pro vided you have requested data and the use of the ccviz program methane his6f contains the configuration and the pair distribution functions generated by the run methane rmc6f will contain an updated configuration If you request periodic saves of the con figurations these will have a number appended as e g methane 23 rmc6f methane SQpartials csv willcontain the calculated partial scattering functions in CSV format methane 501 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 methane PDFpartials csv will contain the calculated partial pair distribution functions in CSV format methane PDF1 csv will contain the calculated and experimental da
130. canBoNv Nurrgo CcvcLoPRoPANE CcsPsaLkaNE CBENZENE LO BENZENE LO CALIZED CBENZENE LOCALIZED CALIZED CBENZENE LOCALIZED CocsraLkvNE BENzENE LOCALIZED CBENZENE LOCALIZED 0 5 LOCALIZED CBENZENE LOCALIZED Nnsp3 CBeNnZzENE LOCALIZED CBENZENE LOCALIZED 5 P3CYCLOBUTANE CCSP3ALKANE Cosp3aLKANE Ccsp3cYCLOBUTANE HEXCEPTONN O S Cocsp3aLKANE Ccsp3cYCLOBUTANE OCO H C O C 0 0 5 PscvcLoBUTANE N NSP2 5 P3CYCLOBUTANE Ccyc LOPROPANE CospsaLkaNE CcspscYCLOBUTANE C cSP3CYCLOBUTANE CocsPsaLkaNE CcsPscvcLoBUTANE CC OCYCLOBUTANONE CosPsaLkaNE CcsPscvcLoBuTaNE OoH 0 c CARBOXYL 0 5 Ccsp2carBONYL Ccsp3cYCLOBUTANE CCSP3CYCLOBUTANE 0 5 0 5 0 5 0 5 0 5 0 5 0 5 0 5 0 5 0 5 LOBUTANE HEXCEPTONN O S LOBUTANE
131. 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 happens 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 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 C 1 Zn 201 1 101 C 201 2 Zn 1 These lines describe the second triplet defined in the data namely C C Zn linkages and 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 sad
132. d distance window constraints 13 Use of coordination number constraints 14 Ability to use model specific polyhedral constraints 15 XML output for data visualisation and analysis 16 Various ancillary tools eg tools to create starting configurations from crystallographic CIF files But we stress that it works perfectly well for liquids and amorphous materials 7 154 RMCProfile Manual v6 5 2 1 3 RMCPROFILE INTRODUCTION This manual is primarily focussed on Version 6 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 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 rewriting New functionality 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 some new tools to perform the file conversion that are described in section 4 15 Version 6 is fully compatible with classic style input files although n
133. d in order for RMCProfile to read it In the course of an RMC refinement RMCProfile calculates Bragg peak intensities and adjusts the configuration to match the measured intensities For more information about using Bragg data please see section 4 13 4 6 Using EXAFS data We are currently working to incorporate EXAFS documentation into this manual but for the time being please see the EXAFS manual at nttp www rmcprofile org imagesFhj 5 51 Rmcprofile exafs manual pdf for more information 4 7 Using potentials As discussed in section 2 5 using well parameterised interatomic potentials judiciously can play a role when the short distance part of the pair distribution function is dominated by intramolecular distances that are not of primary interest in a a study 58 154 RMCProfile Manual v6 5 2 4 7 USING POTENTIALS 4 7 4 Bond stretching potential We assume that the energy required to stretch a bond can be described using a Morse potential D 1 exp a r rg 4 21 The function is written in this way so that the energy is zero at the origin as itis for simple polynomial expansions of the bond stretching energy Aside from the r parameter The Morse function has three adjustable parameters namely 0 to specify the length of the bond D to specify the energy required to break the bond and o which plays a role in specifying the curvature of the potential energy function around the minimum Following the
134. data into the csv format realise writing this that haven t thought about when you have several data files another tweak 8 also don t have some of this output stuff working with x rays so need to chat about this another tweak 9 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 152 154 RMCProfile Manual v6 5 2 APPENDIX E REFERENCES Appendix E 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 17 515 522 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 1723 1730 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 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 N
135. e sums for each atom type smaller numbers give heav ier weighting RIJ Give the bond valence parameters for each atom pair in turn enter O for non bonded pairs These are or dered in the same way as when giving the coeffi cients but in this case you do not include the like atom pairs For a 3 atom configuration you d supply the parameters for pairs 1 2 1 3 and 2 3 in that or der 40 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt BVAL Give the value of B for each atom pair This is usu ally taken as a constant 0 37 Enter 0 for non bonded pairs CUTOFF Give the cut off distances for calculating the bond valence sum for each pair in turn Enter O for non bonded pairs gt SAVE Indicate how often you want an update on the status of the bond valence sums to be printed UPDATE Indicate how often you want the neighbour list which defines which atoms are bonded to each other to be updated CML CCVIZ Instructs the code to run the ccviz program that converts the xml file to an xhtml file The parameter gives the path and name of the ccviz program Ex amples are ccviz if the program is in the same location as you are running RMCProfile from and use local bin ccviz if you are running ceviz from a specific 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 req
136. e 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 materials and crystals with significant thermal disorder rotational disorder of molecular groups and site occupancy 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 le
137. e PDF and it is not consistent with the value obtained from these tables you are again recommended to use the value deduced from the PDF Note however we caution against using distances and angles taken from a standard crystal structure refinement because these are not true bond lengths Crystal structure gives you the mean positions of atoms and the distance between two mean positions is not always the same as the mean instantaneous distance between the two atoms One of the joys PDF based approaches to studying materials is to be able to identify cases where there is a difference between these quantities because it points to the existence of disorder beyond simple thermally induced harmonic atomic motions 2 1 Bond stretching terms Table B 1 Bond stretching terms from the standard MM3 data set D eV CcsPsaLKANE CCSPSALKANE 1 52 2 155 CcsPsaLKkaANE CCSP2ALKENE 1 50 3 024 CcsesaLkaNE CcsP2CARBONYL 1 51 2 304 Mathematically this point is equivalent to the fact that r2 gt n 120 154 RMCProfile Manual v6 5 2 2 1 BOND STRETCHING TERMS CcsPaALKANE CCSPALKYNE 1 47 2 640 8 111 2 275 0 6 0 0 141 2 736 CcsPaaLkaNE NNsPa 1 45 2 544 2 1 45 2 501 Ccsp3aLKANE F FLUORIDE 1 39 2 832 CcspsaLkane ClcHLORIDE 1 79 1 488 CcspsaLkane BrBRoMIDE 1 94 1
138. e are the first two atom types listed in the main configuration file If this is not the case then you will have to re order your main configuration file The coefficients used to calculate the magnetic form factors from equation 2 5 are entered using the lines gt FORMFACTOR Aa B b D This is required for every magnetic atom type Alternatively the gt FORM FACTOR FILE lt name file gt keyword must used an appro priate file included in the directory The magnitudes of the magnetic moments for each atom type are entered using the gt MAGNETIC MOMENTS keyword The numbers should be entered in the correct order gt MAX SPIN MOVEMENT line gives the value of described in Section 2 10 2 a small value 20 1 is appropriate gt SPIN MOVE RATE describes the fraction of moves generated that will change the spin configuration For example a spin move rate of 0 0 will result in no spin moves being generated and the magnetic structure will remain unchanged Alternatively a spin move rate of 1 0 assuming no swap moves are being used will result in only magnetic moves being pro duced RMCProfile has the facility for the spin move rate to be automatically varied during the course of the refinement This is implemented using the gt vARY SPIN MOVE RATE keyword The default is not to vary the rate but this can be explicitly included using the gt NO VARY MOVE RATE keyword
139. e concentration of the relevant magnetic specices p is the number density of magnetic atoms e me and c carry their usual meanings gJ is the magnetic moment and the magnetic 15 154 RMCProfile Manual v6 5 2 2 10 MAGNETIC STRUCTURE MODELLING 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 ajp Q exp iQ vj 2 2 where the magnetic interaction vector is given by m QQ an 2 3 and mj is the spin vector of the magnetic species j The magnetic scattering amplitudes p Q are related to the magnetic form factors e 7594f Q 2 4 2m 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 2 10 3 Implementation The various keywords and required parameters are listed in section 4 1 below and are not repeated here The basic idea is that all spin related files run from a slightly different user specified stem to t
140. e name extensions and these are TBLOr tbl files produced by GSAS we anticipate that many users of RMCProfile will have run a prior Rietveld refinement cif CIF crystal information format format favoured by many databases such as the Inorganic Crystal Structure Database SFF or sff our own simple file format subsubsection 6 1 1 CFG Or cfg RMC v3 configuration file or cfgcom Input file for the crystal configuration generation tool subsection 6 1 2 The output files all have the same seed name For example the command data2config diag cssr rmc f nacl cif will produce the configuration files nacl cssrandnacl rmc f and the diagnostics file nac1 out Simply typing the command data2config 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 6 1 1 Setting up for Bragg scattering data from GSAS If you are including the Bragg scattering data explicitly within your RMC analysis you will need to have performed a GSAS Rietveld refinement and provide the back inst and bragg files see Section 4 5 102 154 RMCProfile Manual v6 5 2 6 1 DATA PREPARATION TOOLS These files will be automatically generated if your crystal structure file type is of type TBL a GSAS table file and your working directly also contains the corresponding GSAS and LST files
141. e of and gt symbols These are used to define the type of data Anything after these characters is treated as 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 e g 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 below b where the are followed by some data for example MATERIAL Quartz The parser will know what to expect whether characters or numbers 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 33 the FLAGS keyword line is followed by a set of lines for which each subordinate keyword is merely a di rective 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
142. e 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 zirco nium atom and the ozr file contains a list of the zirconium neighbours around each oxygen atom Similarly the po file contains list of oxygen neighbours around each phosphorous atom and the op file contains list of the phosphorous neighbours around each oxygen atom All of these neigh bour files should be generated using the neighbour list program supplied with RMCProfile and described in section 6 1 4 10 8 The ZrW5Og 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 ZrW2Og This restraint differs from the ZrP2O 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 and files supplied The 1 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 100 and then the weighting for the octahedral angle restraint e 300 The following line must contain the ideal bond distance to be used the weighting for t
143. e stem name In addition to these will be files containing the scattering data and the pair distribution function There no constraints on the names of these files which are given in the dat file These data files will be described in section 4 3 These files are described in the chapters and sections indicated above 3 3 Running RMCProfile To run RMCProfile execute the following shell command rmcprofile methane gt methane log The part of the line gt methane 1og tells the command to direct the standard output to a specified file here called methane 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 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 methane gt methane log 30 154 RMCProfile Manual v6 5 2 3 4 OUTPUT FILES Otherwise you need to give the full name of the program file including all the directory information On Windows if you always run RMCProfile
144. e 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 c g section Then the chemical symbol for each atomic species in the configuration 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
145. eans 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 stage is divorced 4 154 RMCProfile Manual v6 5 2 1 2 WHAT AND WHY OF RMC 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 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
146. ected regularly during an RMCProfile minimisation to ensure that they are not restricting the model excessively 4 10 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 SiO SrTiOs CD4 SFe 4 PZT ZrP207 ZrW20g MN RF DN KON AgCN 13 Zn CN 2 70 154 RMCProfile Manual v6 5 2 4 10 POLYHEDRAL RESTRAINTS 14 C4Fg 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 the data weighting is always higher if this is not done then the restraint will become a constraint and the data will be ignored and the resulting configuration biased Please no
147. ed neutron G r neutron total scattering 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 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 84 154 RMCProfile Manual v6 5 2 4 14 RMCPROFILE VERSION 3 FILES weighting factors i e 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 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 can 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 crystallin
148. ed in the potential RMCP rofile enables the use of two types of potentials namely for stretching of bonds and flexing of bond angles With proper weighting of the contribution of the potential with respect to 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 In fact the weighting used on the potentials within RMCP 21 1 is tied with the temperature of the experiment and if the weightings on the experimental data are associated with experimental errors the RMC method will give the correct balance between the dat and potentials 2 6 Bond valence constraints In the early stages of an RMCProfile refinement any atomic move which broadens the function like peaks in the correlation function calculated from the crystal structure will be accepted as an improvement to the fit and this can cause regions of extreme disorder in the configuration which are subsequently very difficult to correct The use of bond valence constraints which maintain the bond valence sum to within a certain window of the ideal value can help to prevent this unphysical effect Bond valence constraints can be particularly useful when several components in the system have very similar contributions to the scattering functions a principle the relevant author subscribes to 13 154 RMCProfile 2 w6 MQD
149. eighting for this bond restraint 100 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 both of these files should be generated using neighbour_list program supplied with RMCProfile and described in section 6 1 4 10 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 agc nc and agn files supplied The po1y file contains 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 C N bond distance to be used and the weighting for this bond restraint The next line must contain the ideal bond distance to be used and the weighting for this bond restraint The 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
150. em name as your dat file The first is the poly file which contains the weights for the restraint 96 154 RMCProfile Manual v6 5 2 5 8 EXAMPLE OF USING MAGNETISM title 1 613 100 300 The first line is a title line which is ignored and the second line contains the ideal Si O bond length and the weightings for the bond restraint and the tetrahedral angle restraint The weights are simple multipliers with larger numbers giving heavier weighting so in this case the angle restraint is given the higher weight The format of this file changes slightly for different restraints please see section 4 10 Next are the neighbours files These differ with different restraints again please see section 4 10 For the 510 restraint you will need two files sio and osi The file contains list neighbours around each Si atom and looks like this 5184 1 4 5509 7887 10801 14392 2 4 5510 7885 10802 14393 3 4 5511 7886 10803 14394 4 4 5512 7890 10804 14395 5 4 5513 7888 10805 14396 6 4 5514 7889 10806 14397 7 4 5515 7893 10807 14398 8 4 5516 7891 10808 14399 9 4 5517 7892 10809 14400 10 4 5518 7896 10810 14401 The first line is the number of Si atoms the subsequent lines structured as atom ber number of O neighbours and the atom numbers of those neighbours in the configuration file Similarly the osi file contains the Si neighbours around each 10368 5185 2 865 1423 5186 2 86
151. ement is not yet perfect 5 4 Example of using potentials 5 4 1 Example of KCN In the examples of KCN given above we used a potential to bind the atoms in the C N molecular anion This was controlled in the data file using the keyword block 92 154 RMCProfile Manual v6 5 2 5 4 EXAMPLE OF USING POTENTIALS 1 4 Intensity EN T 6 8 10 12 14 16 18 20 22 Flight time ms Figure 5 3 The Bragg profile for KCN at 50 K in its ordered phase comparing experimental data black line and the fitted function from the RMC model red line POTENTIALS gt STRETCH 8 86 eV 1 16 Ang gt STRETCH_SEARCH 20 gt TEMPERATURE 250 K This is a relatively simple example because we have only one potential involving the bond stretch In this example the potential parameters are chosen to give the correct stretch frequency When combined with the sample temperature the potential energy function will give a width of the peak in the PDF of the correct width mode complicated example is for the crystal of ZrP207 The keyword block for the potentials is POTENTIALS gt STRETCH P 8 86 eV 1 52 Ang gt STRETCH Zr 8 86 eV 2 05 Ang gt STRETCH_SEARCH 10 gt ANGLE 20
152. en erator program doesn t do this Default is not to sort SWAP 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 TEMPERATURE Requires text to denote the temperature of the material being studied This is used for metadata and is not compulsory Units are not parsed TIME_LIMIT Requires time limit in minutes for the job TITLE Requires text to act as a title for the run This is used for metadata and is not compulsory 38 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE XRAY_RECIPROCAL_SPACE_DATA Introduces a block of data concerning a set of X ray scattering data Text can follow the but will be ignored This keyword must be followed by a block of subordinate keywords Do not pro vide 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 subor dinate keywords is given under the corresponding major keyw
153. ensity you provide While it can be used to produce a random configuration a significant amount of time can be saved by applying closest approach constraints producing a starting configuration in which none of the atoms are too close together The program asks for the information it requires and writes out both and files Note to obtain a random configuration the user should enter zeroes when asked for distances 6 2 analysis tools 6 2 1 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 6 2 2 rmcplot This a basic plotting program that can be used to plot information contained in the out braggout file produced by RMCProfile provided at least one save cycle has been completed It requires an X server to be running and can be run on the command line by typing rmcplot bat stem name gt gt where stem name gt gt is replaced by the RMCProfile run name such as rmcsf6 190k in the above example In the plot interface left click allows you to zoom right click resets the view and middle mouse button exits from cursor 107 154 Manual v6 5 2 6 3 CML BASED ANALYSIS TOOLS 6 2 3 Atomeye This program has not been written by ourselves or any of the other RMC developers but is supplied with RM
154. erate configurations containing the number of unit cells specified by the user will be explained later when fitting against the neutron total scattering data it is necessary to take account of the finite range of the pair distribution function when performing the required Fourier transform RMCProfile handles this automatically but the shorter the range of distances in the pair distribution function the more degraded is the Fourier transform 23 154 RMCProfile Manual v6 5 2 2 13 XML OUTPUT FILES 2 12 3 Non crystalline systems Obtaining a starting structure for a non crystalline material is a challenge that may take us outside of RMCProfile There are several approaches depending on the material and on the scope of data available The standard RMC approach is to simply throw the atoms into a box at random and let the RMC method arrange them appropriately We have a tool which can do this and can also go one step further and produce starting configurations which do not violate closest approach constraints This tool is called dwbuild and it is discussed further in section 6 1 Another approach to generate a random starting configuration is to run 1 1 without data or constraints which will randomise an initially ordered configuration which can be generated from a real or trial crystal structure using the approach outlined above One important point is to get the density correct but this should already have been deter
155. ere bj is the scattering factor for atom labelled 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 114 154 Manual v6 5 2 1 1 TOTAL SCATTERING scattered beam can change through the scattering process For coherent scattering i e where atoms of the same type scatter the same way this can be rewritten as 3 Y exp iQ 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 19 rj If we consider an atom to have a mean position we can write the average as exp iQ exp iQ 5 plr exp iQ r dr A 4 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
156. eter that gives the maximum rotation of the magnetic spin in any RMC step gt 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 SPIN MOVE RATE keyword is not given 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 43 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE 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 NEUTRON REAL SPACE DATA DATA TYPE Gives the type of data options are G r T r D r together with the word normalised normalized for functions that are scaled by the neu tron scattering coefficient Y c cjb b to give limiting values of 1 depending on the function This is ex plained in more detail in Section X 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
157. eutron total scattering method simultaneous de termination 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 materi als with RMC a new implementation of the algorithm in C Journal of Physics Condensed Matter 17 51 513 2005 9 Tucker M T Dove and D 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 Q Hui M T Dove M G Tucker S A T Redfern D A Keen Neutron total scattering and reverse Monte Carlo study of cation ordering CaySr 1 x TiOs Journal of Physics Con densed Matter 19 art no 335214 2007 153 154 RMCProfile Manual v6 5 2 11 S T Norberg M G Tucker S Hull Bond valence sum a new soft chemical constraint for RMCProfile Journal of Applied Crystallography 42 179 184 2009 12 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 13 An introduction t
158. ew features are not accessible via this route The classic file formats are described in the Version 5 manual 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 least because we do not guarantee support for classic file formats forever 8 154 RMCProfile Manual v6 5 2 CHAPTER 2 CAPABILITIES Chapter 2 Capabilities 2 1 Fitting neutron and X ray total scattering data The RMC modelling method was developed specifically to fit neutron and X ray total scattering data and these data are still the key experimental data for RMCProfile Total scattering i e the Bragg and diffuse scattering collected ideally as an integration over all scattered energies at constant scattering vector 47 sin 0 A provides the information which allows RMCProfile to investi gate deviations from the average crystal structure These data are measured by neutron or X ray diffraction but their collection and treatment is more demanding than a routine powder diffraction experiment for Bragg profile analysis through for example Rietveld refinement This is for a number of reasons 1 The data should be collected over as wide a range of scattering vectors as possible and ex tending to high Q This explains the early dominance of neutron diffraction and in particular time of
159. file in the tutorial folder This helps you check everything is working and leads you through some of the common features of the program This manual aims to tell you most of what you need to know about RMCProfile program together with appropriate background is an approach that will require some investment on the part of the user at both the data collection and analysis stages Accordingly you probably ought to read most of this manual before you start But we know you won t want to so hopefully we have arranged it so that this is not quite as challenging as it might seem at this point If you are one of those people who only want to read a manual when necessary and just want to get things running please just look for the rmcprofile_tutorial pdf file in the tutorial folder This helps you check everything is working and leads you through some of the common features of the program We would point out that RMCProfile is still a work in progress and we have not yet reached the stage where next versions are merely minor iterations from previous versions This manual is copyright by the program authors and developers But because this is a work in progress regrettably there will be some things that are not yet properly documented 3 154 RMCProfile Manual v6 5 2 1 2 WHAT AND WHY OF RMC 1 2 The what is and why of the Reverse Monte Carlo method 1 2 1 The what is in a nutshell The Revers
160. has the form File Generated using stog version 4 1 January 2010 Title KCN in CCR II at 250K I 12Wx34H chop 19302 00ff 1939 Generating user martin Users martin Research rmc KCN 2 Scattering function file File directory Data date 17 2003 12 04 47 stog date 25 01 2010 stog time 12 11 27 Number of points 2469 0 51000000000000001 0 51415966245250289 9 54305797480000176 003 0 53000000000000003 0 50451782866197492 4 84622437520000008 003 0 55000000000000004 0 50557809724236857 3 60939646880000008 003 0 56999999999999995 0 51164861557939501 3 11133462599999999 003 0 58999999999999997 0 51200039215334059 2 61025113720000012 003 0 60999999999999999 0 50293028481557944 2 29396395120000027 003 0 63000000000000000 0 50412099867804050 2 13825509799999997 003 In this case are using a that contains metadata the lines beginning with the character 5 1 2 Data file In the input data file the scattering data are handled using the following keyword block NEUTRON 88 154 1 RMCProfile Manual v6 5 2 5 1 USING SCATTERING DATA Intensity 4 6 8 10 Scattering vector Q 7 Figure 5 1 The scattering function for KCN comparing experimental data black line and the fitted function from the RMC model red line gt FILENA
161. hat 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 are normalised 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 0 2 16 2 Bexp bQ 167 C exp 167 D 2 5 where A B b 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 9 The order the magnetic atoms the 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 16 154 RMCProfile Manual v6 5 2 2 10 MAGNETIC STRUCTURE MODELLING 4 In general magnetic structure refinement takes a substantially longer time than nuclear re finement and there is a significant degree of interplay between the nuclear and magne
162. he installation and initial runs of RMCProfile For completeness however the instructions are also supplied below and on www rmcprofile org RMCProfile 15 provided as a single executable that is designed 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 simply follow the instructions below To install RMCProfile Windows machine 1 Unzip the file once it has downloaded 2 Copy the whole RMCProfile folder to a more permanent home such as NRMCProfile This folder should contain two subfolders exe and tutorial and file called 11 setup bat 3 Run the program by double clicking on the RMCProfile setup bat file This should bring up a command prompt window called RMCProfile Note these instructions should work for Windows XP and 7 There may be problems with file per missions on Windows Vista and we have heard some reports of issues with the path settings in Windows 8 If you encounter these please get in touch To install RMCProfile on a Mac OS X machine 1 Unzip the file once it has downloaded your browser may have done this for you 2 Copy the whole RMCProfile folder to your Applications folder This should make a folder Ap plications RMCProfile which contains three subfolders exe libs and tutorial and a file called RMCPRofile setup command 3 Run the program b
163. he user gt 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 gt FITTED SCALE 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 gt START POINT Start point of the data provided as an integer gt STOG 1 If specified the data file was generated by the STOG program for converting total scattering data to PDF data gt WEIGHT Parameter that weights the data in the simulation POTENTIALS gt ANGLE 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 label 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 in units of deg followed by the two bond lengths in units of Ang which must be stated gt Requests the generation of bond angle histograms in steps of bond angle and the cosine of the bond angle The required step can be selected by using the angle lt value gt option 46 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt ANGLE_SEARCH Give the r
164. hem The two lines containing the number of atoms and number of bonds 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 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 1 Zn 2 44 gt d C 6 10 C 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 lt snip gt lines replace similar data removed for the sake of brevity 61 154 RMCProfile Manual v6 5 2 4 7 USING POTENTIALS 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
165. hese values are used when supplying the keyword to RMCProfile Ideal bond lengths d may be calculated using these values V dj Bin Where 0 37 valence coordination number central atom should be noted that this calculation assumes a regular coordination environment i e the valence of atom would be satisfied with CN equal bonds of length dj Importantly the bond valence sum for an atom can be calculated as the sum of the valences of the individual bonds C 2 146 154 RMCProfile Manual v6 5 2 3 1 VALUES FOR BOND VALENCE SUM CALCULATION Table C 1 Bond valence parameters Cation 1 1 2 24 2 13 2 63 Mn IV 1 753 1 71 2 13 Ag 1 805 1 80 2 09 Mn VII 1 79 1 72 2417 1 651 1 545 2 03 1 907 1 81 2 28 2 11 2 00 248 Nill 1 361 1 37 1 75 1 789 170 2 16 1 432 1 36 1 8 AsV 1 767 1 62 2 14 1 8 1 677 2 15 Au 1 833 1 81 2 17 1 911 1 87 2 27 Bill 1 371 131 1 74 2 117 2 008 2 492 Ba Il 2 29 219 2 69 Nill 1 654 1 599 2 02 Bell 1 381 1 28 1 76 Os IV 1811 172 2 19 Bi IIl 2 09 1 99 248 PV 1 604 1 521 1 99 Bi V 2 06 1 07 244 2 112 2 03 2 53 2 08 1 06 246 PblV 2 042 1 94 243 1 81 1 72 2 19 1 792 1 74 2 05 1 39 1 32 1 76 Prill 2 135 2 022 2 5 Call 1 967 1 842 2 37 Ptll 1 76
166. his bond restraint and then the weighting for the tetrahedral angle restraint The zro file contains 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 6 1 4 10 9 The 4 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 To use this restraint option 9 needs to be specified in the dat file and and op files supplied The 1 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 100 and then the weighting for the octahedral angle restraint 300 The file contains a list of oxygen neighbours around each phosphorous atom and the op file contains 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 6 1 73 15
167. icant 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 3 2 RMCProfile nutshell In more detail RMCProfile offers the following features 1 Support for large atomic configurations 2 Ability to model spin configurations for magnetic materials 3 Ability to study systems with site disorder such as cation disorder or vacancy inclusion 4 Ability to fit both neutron and x ray total scattering data allowing the use of more than one dataset for each experiment type 5 Ability to fit simultaneously the real space pair distribution function obtained by Fourier trans form of neutron total scattering data 6 Ability to fit the Bragg profile directly as well as the total scattering 7 Ability to include EXAFS data in the RMC method 8 Use of generalised molecular potential energy based constraints for bond lengths and angles 9 On the fly calculation of bond angle distribution histograms and bond orientation maps 10 On the fly calculation of various average quantities such as mean bond lengths mean bond angles mean bond orientation spherical harmonics and mean bond Kubic harmonic values 11 Ability to use bond valence sums 12 Use of closest approach an
168. ich has limiting values 2 G r 0 0 G r oo 4 5 4 3 2 Neutron scattering function The scattering function and the PDF G r are related by Note that this differs from the definition by Keen by a normalisation factor we will discuss scaling by normalisation factors later According to the definitions discussed by Keen the functions commonly written as i Q and F Q are synonymous The authors of this manual tend to use both functions 52 154 RMCProfile Manual v6 5 2 4 3 USING EXPERIMENTAL DATA B _ T 2 sin Qr F Q dr 4 6 4 7 7 2mp j 7 Qr For dense materials the scattering function F Q has limiting values 0 2 0 4 8 The scattering factor can be written in a form with a constant offset to give 2 S Q ss 4 9 j which has limiting values 2 S Q gt 0 x 2 S Q 4 10 4 3 3 Alternative forms of the pair distribution function It is common to use two other definitions of the PDF functions E Qi Q sin Qr dQ 4 4 11 and 2 T r D r 4arp sh 4arpG 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
169. ighbours 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 neighbours 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 nearest neighbour distances with four oxygen atoms arranged in 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 Si O Si angle of around 145 Although this is 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 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 5 154 RMCProfile Manual v6 5 2 1 3
170. imensionless Nember of neusten chisq 44 2468 cmlUnits dimensionless reciprocal space data sets 0 0097 cmlUnits dimensionless Number of neutron total scattering intensity data Partial PDF functions sets whether S Q Abscissa rmeprofile riunits A or Qi Q S Q functions ere of species now Numbers of atoms Abscissa rmcprofile Q units invAng type Numbers of atoms of PDF total each type in order of m mmeprofile calculatedTotalPDF units dimensionless 100 rmcprofile experimentalTotalPD F units dimensionless 90 meprofidiferencePDF units dimensionless 2 7 definition to be supplied Number of different atomic species M Number of different atomic species in the RMC Number of different 50 100 atomic species the Abscissa rmcprofile rlunits Angstrom RMC configuration PDF total Data offset flag Show Flag to determine whether L Abscissa rmeprofile rlunits Angstrom motio apply a data offset gt Created using ccViz by Toby White lt tow uszla me See for more information Figure 6 2 Portion of the XHTML file generated by ccViz 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 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 vie
171. ing 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 Safarit for the mac and windows platforms or Firefox for mac windows and linux platforms Older browsers or modern browsers that do not conform to 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 5http uszla me uk space about http www apple com safari 5http www mozilla com firefox 108 154 RMCProfile Manual v6 5 2 6 3 CML BASED ANALYSIS TOOLS rmcprofile Output nitial Metadata et m Labels for the different de creator atom types with order Matt Tucker o ga Dave Keen Andrew Goodwin Qun Hui Martin Dove consistent with the order Code name of atoms the Code URL http www configuration file 2 Code publication URL od 1088 0953 8984 19 33 335218 IUE 280004 version with keyword driven input file CML output Bragg profile background Run start time 00 24 03 parameters Material
172. ing data McGreevy amp Pusztai 1988 McGreevy 1995 Mellerg rd 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 and the corresponding calculated quantity as We then define an agreement factor as 2 y 20 7 where we sum over all data points labelled by 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 2 the change to the configuration is accepted On the other hand if the change to the configuration causes x to increase by an amount 2 the change is not automatically rejected but accepted with the probability P exp Axt 2 21 This ensures the model does not get trapped local minimum and enables the model to converge towards the global minimum In the RMC me
173. integer FILENAME Filename containing the data FIT TYPE Gives the function that is fitted options are F Q Q i Q Qi Q or S 0 together with the word normalised normalized for functions that are scaled by the neutron scattering coefficient c cjbibj to give limiting values of 1 depending on the func tion This is explained in more detail in section 4 3 5 FITTED OFFSET If specified this instructs the program to fit the offset value provided for this set of data Default is not to fit FITTED SCALE Instructs the program to fit a scale factor for the scat tering data Default is not to fit 45 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt GUDRUN If specified the data file was generated by the Gu drun data reduction suite and contains errors on each point gt NEUTRON_COEFFICIENTS 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 30 The default values are cal culated by the code if this keyword is not given see section 4 2 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 t
174. ion 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 gt RESOLUTION CONVOLUTION Instruct the program to use the convolution the ex perimental neutron reciprocal space data with the ex perimental resolution function The default is not to use the convolution gt SAVE CONFIGURATIONS Instruct the program to outputs a separate configura tion file at each save point during the run This is used in cases where it is necessary to collect multiple con figuration files at equilibrium for analysis The different files are numbered e g as rmc6 01 rmc6f_02 etc The default is not to output these files MAGNETISM FORM FACTOR Atom number followed by the seven coefficients for the expression for the magnetic form factor The user will need to provide either this keyword line or the FORM FACTOR FILE keyword line gt FORM FACTOR FILE File containing the magnetic form factors The user will need to provide either this keyword line or the FORM FACTOR keyword line gt MAGNETISM FILE STEM Stem for the associated with magnetic spins gt MAGNETIC_ATOMS 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 gt MAX SPIN MOVEMENT Param
175. is also possible to provide this information via a text file with the same stem name as your dat file and the extension bvs A file for the same example as given above would look like this Y 3 atom 1 Zr 4 atom 2 2 atom 3 0 055 0 055 0 140 chi 2 weights for each type 00 0 Y Zr Rij B cut off distance 2 019 0 37 3 2 Y O 1 928 0 37 3 2 Zr O 400000 intermediate save 200000 neighbour list update 69 154 RMCProfile Manual v6 5 2 4 9 USING CONSTRAINTS AND RESTRAINTS 4 9 Using constraints and restraints Constraints and restraints are valuable ways to direct the RMCProfile run away from unphysical models It should be born in mind however that the overriding ethos of RMC is to produce atomistic models from experimental data and as such the constraints and restraints should play a lesser role than the data in any RMCProfile run The choice of the relative weighting of the constraint s and restraint s with respect to the data is very important and optimum values are often only achieved through trial and error For example when using polyhedral restraints described in the following section it is sometimes beneficial to weight them quite strongly at the start of an RMCProfile minimisation until the model is fitting the data reasonably and then to reduce the weighting so that the data now dominates the choice of preferred atom moves Similarly distance window constraints should be insp
176. is an issue Finally the sigma weight for the Bragg profile is supplied 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 1 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 get in touch 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 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 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 8
177. k that we have carried out on D3Co CN g Hydrogen bonding transition and isotope dependent negative thermal expan sion in H3Co CN g D A Keen M T Dove J S O Evans A L Goodwin L Peters and M G Tucker J Phys Condensed Matter 2010 The structure of this material consists of three interpenetrating lattices each with a distorted cubic topology with octahedrally co ordinated Co atoms at the corners of the cubes linked to each other 0 linkages The interest in this material is in the nature of the hydrogen bonding and by implication the location of the hydrogen atom and how to explain the smaller negative thermal expansion of this material when contrasted with the colos sal thermal expansion in the isostructural material Neutron total scattering data were obtained from at three temperatures and modelled using RMCProfile using distance window constraints to maintain the topology of the structure whilst allowing flexibility of the linkages It was found that as the temperature increased the locations of the deuterium atoms moved from the linkage centre defined by the neighbouring N N atoms such that the density of deuterium atoms peaked preferentially either side of the centre but with no reduction in overall symmetry This shows that the material becomes increasingly molecular as temperature is increased allowing the linkage vibrations to decouple and thus reduce the overall degree of the
178. l having dimensions x Ny x the three integers range in value from 0 Nx 1 0 1 and 0 Nz 1 respectively Note that if the optional integer giving the label of the atom the origin cell is included previous input quantity these three integers must follow that integer attt ta 12 There are as many atoms lines there are atoms There is no termination line If the number of atoms is given the Number of atoms line the lines will be counted as 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 77 154 RMCProfile Manual v6 5 2 4 11 RMC VERSION 6 FORMAT CONFIGURATION FILES 4 11 2 Version 6f format histogram file Normally users do not create the histogram files themselves but instead they are generated by successive runs of RMCProfile However it is useful to understand the format of this file to enable it to be
179. l v6 5 2 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 7 subordinate keyword to the keyword block allowing rmcprofile to automatically generate the xhtml file from the xml file There are certain requirements for this to work 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 5 Fixed some bugs on the way 6 Tracked down the causes of occasional bus errors segmentation faults 7 Added data_type and fit_type to the xml file output 8 Tweaked some of the output messages v6 3 3 1 Some small bug fixes eg getting the wrong name for the new configuration 2 Completed the writing of his6f files I hadn t appreciated that they weren t completed 3 Written the ability to read his6f files not having done this before was an oversight 4 Some small rearrangements with the storage of variables to make coding easier 5 Some new subroutines and one new file exists which are not used by v6 3
180. le 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 0 8 10 10 8 8 12 12 The first line gives the minimum value of the d spacing and the remaining three lines give the limiting values of h and respectively This file is not necessary if either of the gt DMIN or gt QMIN subordinate keywords supplied within the keyword block under the BRAGG keyword RMCProfile 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 13 2 The bragg back and inst files 4 13 2 bragg The Bragg scattering data is contained within with extension bragg It has the format appro priate for time of flight diffractometers an example being 1818 2 6 7798 274 9949 Sample data file 4 983635 4 38 02 4 987625 4 33 02 4 991615 4 27 02 4 995605 4 23 02 4 999600 4 26 02 5 003600 4 30 02 5 007606 4 35 02 21 215999 2 34E 03 21
181. ly the information concerned with the additional data for the histograms from which the pair distribution functions are calculated 78 154 RMCProfile Manual v6 5 2 4 12 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 12 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 gr for a G r PDF file or sq for the neutron scattering S Q file 4 12 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
182. ly you will have to do some hand work 4 7 6 Visualisation of bond orientation distribution functions RMCProfile allows for easy plotting of bond orientation distribution functions 63 154 RMCProfile Manual v6 5 2 4 7 USING POTENTIALS Figure 4 1 Example of a stereographic representation of the bond orientation function generated by RMCProfile 4 7 6a Histogram file RMCProfile produces histograms of the number of bonds over the non uniform grid of 0 and polar coordinates defined using the convention used in the physics community This file is given a name of the form name bondodf_n where lt name gt is the root name of the 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 0 and is not normalised for the size of the solid angle The grid is in uniform steps of and Ao with grid size of 40 x 80 cells 4 7 6b PPM plot file By using the 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 name 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
183. meta data keywords case independent are investigators affiliation material phase chemical formula title purpose keywords temperature pressure note and comment Note that the metadata values can have several words lt value gt Creates a spherical nanoparticle with radius given as the essential lt value gt parameter noannotate 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 rect Request the program to form a C centred orthorhombic cell from an initial hexgonal or trigonal set of axes This will work even if your cell is not strictly with a set of hexagonal lattice parameters rmc3 Write the classic version 3 configuration file output filename has the extension cfg This flag is switched off if the input file is itself a c g 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 xmc f size value Usually data2contig will ask for the user for three integers with which to scale the starting structure in each direction to create the configuration Using this flag with the required parameter will set the supercell to have dimensions along
184. method should be sufficient to drive a simulation without needing help from additional potential energy functions and in particular adding interatomic potentials to help drive the simulation moves us away from a purely data driven approach However we have found that there are cases where the use of interatomic potentials may 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 definitely 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 inter atomic contacts that are not includ
185. mined in order to convert the total scattering function to a pair distribution function There are known problems with this approach and the RMC method will need to be used with care If you have some trial interatomic potentials you could use a molecular dynamics or Monte Carlo method to generate a starting structure Even a crude model might be adequate to give a trial con figuration that will be good enough Our data2config tool can create configuration files of the right format from some configuration file formats that are generated by standard molecular dynam ics simulations and if there is demand more file formats can be incorporated into the functionality of data2config 2 13 XML output files RMCProfile produces a number of standard output files in text form It also generate a file con taining 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 XML is a way of writing documents in which each piece of information is enclosed with descriptive tags as will be demonstrated below XML files not designed to be read by humans although if a human wants to read and XML file the contents should be reasonably well self described but instead should be easily readable by computer programs And herein lies the power of XML which has enabled us to build analysis tools that will be described later in section 6 3
186. n be switched off using a keyword in the main dat file 29 154 RMCProfile Manual v6 5 2 3 3 RUNNING RMCPROFILE methane inst containing information on the instrument resolution function in the format as pro vided the GSAS Rietveld refinement code subsubsection 4 13 2c compulsory if using the Bragg scattering as data methane hk1l containing information on the range of Bragg peaks to be considered in the analysis of the Bragg diffraction data This file is not required if the information is provided in the main dat file subsubsection 4 13 1a methane dw containing information on the distance window constraint as described in section 2 4 this has now been incorporated into the main dat file but is included here as it is still possible to use the dw file methane bonds containing lists of all the bonds used in the interatomic potentials If this file is not available it will be automatically generated for re use by RMCProfile we recommend that this file be generated using a well ordered configuration Subsection 4 7 4 methane triplets containing lists of all the bond angles used in the interatomic potentials If this file is not available it will be automatically generated for re use by RMCProfile we recommend that this file be generated using a well ordered configuration subsection 4 7 5 The methane stem part of the file names can be anything you like but as in this example this group of files must have the sam
187. nate keyword In this case the is required because we plan to add a sory parameter END POINT End point of the data an integer FILENAME Filename containing the data FIT TYPE Reserved for the function that is fitted the only option today is F Q FITTED OFFSET If specified this instructs the program to fit the offset value provided for this set of data Default is not to fit FITTED SCALE Instructs the program to fit a scale factor for the data Default is not to fit 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 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 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 the user START POINT Start point of the data provided as an integer WEIGHT Parameter that weights the data in the simulation 48 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE Note that the order of the atom pairs is set by the order of atoms in the configu
188. nd second is the format of the configuration file Let s deal with the configuration file first We have created the data2config tool subsection 6 1 1 to make this simple You start with a classic c g file run the command data2config lt whatever gt cfg 86 154 RMCProfile Manual v6 5 2 4 15 UPGRADE TO V6 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 turn to subsection 6 1 1 To convert the dat file to the new v6 format we provide the rmc326 command 22 You simply need to run the command rmc326 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 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
189. nd 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 Ti O 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 6 1 72 154 Manual v6 5 2 4 10 POLYHEDRAL RESTRAINTS 4 10 7 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 ZrP2O To use this re straint option 7 needs to be specified in the dat file and poly zro ozr po and op files supplied The 1 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 i e 100 and then the weighting for the octahedral angl
190. ne Csp3 C Alkane Csp3 HH Hydrogen CH 109 800 7 365 Camide C atkane Csp3 Namide 109 500 10 611 Camide Catkane Csp3 Nammonium 110 740 13 045 1 109 490 6 741 N Amide 109 500 10 611 Ccarboxyi CaAlkane Csp3 HHyarogen CH 109 490 6 741 CPhenyr7 Calkane Csp3 HHydrogen CH 109 500 6 866 CAlkene His TrpC C C Alkane Csp3 H Hydrogen CH 109 500 6 866 NAmide CAlkane Csp3 HH Hydrogen CH 111 000 9 487 Nammonium CAlkane Csp3 108 800 6 242 143 154 RMCProfile Manual v6 5 2 2 2 BOND BENDING TERMS Nauanidinium C Alkane Csp3 111 000 9 487 Oatcohol Phenol C Alkane Csp3 H Hydrogen CH 110 000 10 236 Ssutfide C alkane Csp3 HHydrogen CH 110 800 9 238 107 600 6 866 114 400 7 115 123 500 10 611 N Amide C Amide O Amide 124 800 13 357 109 300 5 493 119 200 10 611 Catkane Csp3 C carboxyl O carboxylate 125 100 10 611 Ocarboxylate C carboxy Ocarboxylate 134 000 9 987 122 300 5 867 121 70
191. ne contains the name of the file to which you wish the configuration to be written The crystal program is run in a command prompt window in two ways The simplest 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 105 154 RMCProfile Manual v6 5 2 6 1 DATA PREPARATION TOOLS 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 s 6 190k cfgcomis in the current directory or path Note that the data2config tool can both read and generate files in the format used by crystal 6 1 3 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 6 1 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
192. not then their location needs to be en tered after the program name before hitting return i e gsas bragg d my_gsas_exe 6 1 7 neighbour list This program should 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 106 154 Manual v6 5 2 6 2 ANALYSIS TOOLS have the same stem name as the other RMCProfile run files If you use the new molecular restraints this is not required 6 1 8 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 If you use the new molecular restraints this is not required 6 1 9 gaussdist This program reads in an RMC configuration and applies a small shift to each atom to produce a Gaussian distribution around each crystallographic site It also applies a gaussian narrowing to directly bonded atoms in order to produce a starting configuration with a better visual agreement with a measured PDF It asks for the information it needs and produces both cfg and rmc6f files 6 1 10 dwbuild This program builds a non crystalline starting configuration based on a composition and d
193. ntations 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 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 2 10 2 Algorithm Spin orientation moves are implemented within RMCProfile as follows The orientation of each spin the normalised spin vector is treated as a point on the surface of a sphere A random spin move vector 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 configura tions via two real space correlation functions A r 2 ery Smag Q 30M 22000 4 2 Qr Qr fr An a ao qa fo 2 1 where Cy is th
194. ntrol over various options which have assumed values when the file is generated by RMCProfile Yourun bondplot as a simple command within the shell or command interface with no parameters The program will in order ask for the following information 1 The name of the histogram file 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 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 4 7 7 Generation of spherical harmonic function averages RMCProfile automatically computes the mean value and mean squared value and hence the vari ance on values of the spherical harmonics that describe the orientation of a bond We convert the complex numbers to real equivalents by combining the real and imaginary components as Shttp Awww lemkesoft com 65 154 RMCProfile Manual v6 5 2 4 7 USING POTENTIALS gt 0 Y ifm 0 4 26 lt 0
195. o 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 6 1 16 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 y Z 1 2 1 2 2 1 2 x y 1 2 z x 1 2 y 1 2 z 103 154 Manual v6 5 2 6 1 DATA PREPARATION TOOLS atoms 2 Na 0 0 0 0 0 0 Cl 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 6 1 1f Warning Users should be warned that in making the generati
196. o the use of neutron scattering methods in mineral sciences M T Dove European Journal of Mineralogy 14 203 224 2002 14 A 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 119901 4 2005 15 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 16 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 6111 5124 2005 17 M G Tucker A L Goodwin M T Dove D A Keen S A Wells and J S O Evans Negative thermal expansion in 2 208 Mechanisms rigid unit modes and neutron total scattering Physical Review Letters 95 art no 255501 4 pp 2005 18 M Tucker D A Keen J S Evans T Dove Local structure ZzW2Og from neu tron total scattering Journal of Physics Condensed Matter 19 art no 335215 16 pp 2007 19 A L Goodwin M G Tucker M T Dove E R Cope and D A Keen Model
197. ogram calculation is supplied this number should be the same as the spacing of any G r data supplied Then a value of t rue 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 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 time 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 support
198. olume The individual pair distribution functions are defined as Nmn r 4rr pmdr VAS 9 where Nmn r is the number of atoms type n lying within the range of distances between and dr from any atom of type and pm It is common to define the pair distribution function in terms of the new function D r 4xrpoG r A 10 so that Qi Q D r sin Qr dr A 11 The reverse transformation is then given as D r 7 Qi Q sin Qr dr A 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 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 Qi Q to a high value of Q typically of order 30 50 1 in order to achieve the best possible resolution the resolution Ar is given as 27 Qmax where is the maximum value of achieved in the measurement of Qi Q It is also important to appreciate that it is necessary to have an absolute measurement of Qi Q if the result
199. ommunities 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 51 154 Manual v6 5 2 4 3 USING EXPERIMENTAL DATA 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 31 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 where is the number of atoms of type per unit volume We the following limiting cases 0 0 1 4 1 It will be convenient to introduce the number concentration cj where where p is the total number of atoms per unit volume Clearly cj 1 We define an overall PDF by merging all the partial PDFs with appropriate weighting consistent with the concentration and neutron scattering power as r x CiCjbibj gilr 1 4 2 ij where 6 is the scattering factor of atom type The limiting values are 2 G r 0 ss gt 0 4 3 The equation for G r be expressed in a form with a constant offset 2 cicjbibjg r an Y on 4 4 wh
200. on flight time t This is the same x that is minimised by a least squares 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 119 154 RMCProfile Manual 6 B SUGGESTED VALUES FOR INTERATOMIC POTENTIALS Appendix B Suggested values for interatomic potentials This appendix contains recommended values for certain molecular interactions that you might need If you can t find exactly what you need it should be possible to adapt these values The tables below report values taken from the MM3 molecular mechanics database of values For the values of the distances ro you are recommended to check that these are consistent with the position of the corresponding peak in the experimental PDF and if they appear to be significantly different you are recommended to use the distances from the PDF Moreover if you can deduce a bond angle from th
201. on 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 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 to 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 6 1 19 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 n
202. on 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 6 1 2 crystal tool for producing classic format configuration files This program is an alternative to data2config for the generation of a starting configuration of atoms RMCProfile building supercell of a specific crystal structure and writing out a classic version cfg file As you will see below crystal is not as fully featured as data2config but we include it in the distribution as many people still find it useful 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 Email contact details can be obtained from http web me com dove_family martin contact html 104 154 RMCProfile Manual v6 5 2 6 1 DATA PREPARATION TOOLS 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
203. ontains a list of the fluorine neighbours around each carbon atom and the file contains a list of the carbon neighbours around each fluorine atom All of these neighbour files should be generated using the neighbour list program supplied with RMCProfile and described in section 6 1 4 11 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 which reflect a different approach to managing configuration files These are somewhat richer than the classic Version 3 format files described later 4 11 1 Version 6f format configuration file This format is best described with reference to an example file Version 6f format configuration file Metadata tile NaCl in a small box Metadata owner Martin Dove Metadata date 15 02 2009 Metadata material NaCl Metadata comment This is a test configuration Metadata source Solid State Physics text book 75 154 RMCProfile Manual v6 5 2 4 11 RMC VERSION 6 FORMAT CONFIGURATION FILES Number of moves generated Number of moves tried 0 0 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
204. ord 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 merely replicate the default behaviour but can be useful as a record of the user s explicit intentions AVERAGE_COORDINATION_CONSTRAINTS gt Give in order the following parameters central atom type e g 1 neighbour atom type e g 2 the dis tances between which to calculate the coordination number e g 0 2 0 the desired average coordina tion number e g 4 0 and the weighting for this con straint e g 0 0001 the smaller this value the stronger the weighting The 1 refers to the 1st average ordination constraint Duplicate this subordinate key word and append the appropriate number e g gt CAVSTR2 if you have more than one constraint 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 DMIN Give the minimum d spacing value to be used in the analysis of the Bragg diffraction data Users can use the subordinate keyword instead The use of this subordinate keyword will replace the need for the hk1 file 39 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt Give in order
205. ositions 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 within 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 b exp Q rj A 1 wh
206. oximately accounted for via a scaling of the scattering function by the products of x ray form factors this is not an exact procedure however In passing we note that there are several definitions of the PDF in common use this situation will not change primarily because different definitions have their own advantages and there is no single function that captures all the advantages These are described in detail in section 4 3 RMCProfile is capable of using all definitions for input and will convert between conventions for fitting if required We recommend that the functions D r or T r be used as the function for fitting because the errors are spread evenly across all points in the function Be warned though not only are there several different functions different authors use different symbols for these functions We use the symbols described in section 4 3 2 3 Fitting the Bragg profile The headline reason for the existence of RMCProfile is its ability to utilise the information con tained specifically in the Bragg diffraction pattern rather than merely folding it into the normal total scattering pattern The Bragg diffraction contains information about the distribution of atoms on an absolute scale On the other hand the total scattering contains information about the arrangements of atoms relative to each other A determination of the structure of a material requires both types of information Traditionally crystallography of course
207. pe and also averaged over steps The resultant averages namely and are printed in the file with name ile ylm 4 8 Using Bond valence sum To access this functionality you will need to provide the Bvs block of keywords as described in section 4 1 2 in the dat An example is given below 68 154 RMCProfile Manual v6 5 2 4 8 USING BOND VALENCE SUM BVS gt Y Zr gt OXID 3 4 2 gt WEIGHTS 0 055 0 055 0 140 gt RIJ 0 2 019 1 928 gt BVAL 0 0 37 0 37 gt CUTOFF 0 3 2 3 2 gt SAVE 400000 gt UPDATE 200000 The first two subordinate keyword lines define your atom types and their oxidation states These must be in the same order as specified in the dat file The next line gives the weights of the constraint for each atom type The smaller the number the stronger the constraint The subsequent lines give the relevant bond valence parameters for your atom pairs as per Brese and O Keefe Acta Cryst 47 192 197 1991 The ordering of the pairs should be for an example 3 atom configuration given as 1 2 1 3 2 3 Note that unlike when listing coefficients in the main dat file here you do not include like atom pairs Enter zeroes for non bonded pairs The final lines determine how often you want an update on the status of the BVS constraint and how often the neighbour list is recalculated While we recommend the keyword method for simplicity it
208. ragg 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 8 and if you are not interested in crystalline materials you might like to take a look at this code As we have just said the key feature RMCProfile when applied to crystalline materials is that it separately handles both the total scattering and the Bragg scattering Thus it make simul 6 154 RMCProfile Manual v6 5 2 1 3 RMCPROFILE INTRODUCTION taneous 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 materials the information about the distribution of atomic positions is of no value and the struc ture 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 signif
209. range of approximately 0 lt Q lt 25 1 These data have already been convoluted with box function of width 8 88 which is half the box size of our configuration Running the program using the command rmcprofile mno 18 154 RMCProfile Manual v6 5 2 2 10 MAGNETIC STRUCTURE MODELLING we obtain the output file out which includes the fit to data shown in Fig 2 3 There reason able agreement over most values of except between 0 lt lt 1 where the key magnetic structure reflection is not modelled well at all 5 0 0 5 10 15 20 25 1 Figure 2 3 Initial fit to neutron scattering data for MnO Data are shown as solid points the 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 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
210. ration 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 3Note that the order of atoms is set by the configuration file 4 1 5 Example files This is an example of a simulation of RMC refinement of Ag3Co CN 6 Using new input format oe oe 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 NEUTRON REAL SPACE DATA 1 FILENAME ag3cocno 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 M NEUTRON RECIPROCAL SPACE DATA 1 gt FILENAME ag3cocno 300k sq dat gt DATA TYPE S Q gt FIT TYPE Oi Q gt
211. rmal expansion contraction in the material The keyword input for the system described above with atoms given in the order D Co C N might look like this DISTANCE_WINDOW gt MNDIST 2 8 0 0 0 91 01 72 0 2 47 0 gt MXDIST 3 8 001 8 0 2 06 0 2 87 0 The minimum and maximum distances for each pair are given sequentially in the order 1 1 1 2 1 3 1 4 2 2 2 3 etc Therefore in this case the constraint is stating that pair 1 1 two deuterium atoms must be no closer together than 2 8 and no further apart than 3 8 The zero values are 95 154 RMCProfile Manual v6 5 2 5 7 EXAMPLE OF USING POLYHEDRAL RESTRAINTS used when there is no constraint applied to that pair When using the distance window constraint it is extremely important to delete the neighbours files neigh and neighlist when you start a new run or after changing the configuration as these files define the connectivity of your system and must be updated when changes occur 5 6 2 Coordination number Either fixed or average coordination number constraints can be used A fixed coordination number constraint will attempt to drive all or a specified percentage of an atom type to have the desired coordination number The strength of this constraint can be increased by reducing the weighting number and or by narrowing the range over which the coordination number is calculated The weight should be within the range 1 10 2 1 10 9 though values of
212. ro 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 gt START POINT Start point of the data an integer gt STOG 1 If specified the data file was generated by the STOG program for converting total scattering data to PDF data gt WEIGHT Parameter that weights the data in the simulation NEUTRON RECIPROCAL SPACE DATA gt DATA TYPE Gives the type of data options 0 OF Q 0 01 0 or s Q together with the word normalised Or normalized for functions that are scaled by the neutron scattering coefficient c cjb b to give limiting values of 1 depending on the func tion This is explained in more detail in Section X 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 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 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 sory parameter END POINT End point of the data an
213. rom an input dat file POTENTIALS gt STRETCH 4 0 1 15 Ang gt STRETCH Zn 2 0 1 95 Ang gt STRETCH_SEARCH 10 gt ANGLE Zn 4 0 90 0 deg 1 95 1 95 Ang gt ANGLE C 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 zrotation 45 deg we have defined two bonds for and 2 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 association 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 respectively with a tolerance of 1096 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 2 angle of equilibrium value 90 The octahedra are connected via bonds which form part of a linear Zn C C Zn linkage We might want to add a potential to ensure the 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
214. s if the neutron coefficients are given in the input file the example line would be 2 EUTRON_COEFFICIENTS 0 01233 0 00346 0 05535 0 07795 0 00024 0 00776 0 01092 0 06211 0 17496 0 12320 These values are calculated as follows the first referring to pairings is equal to 0 5922 x 3 16 and the second referring to Ag Co pairings is equal to 2 0 5922 x 3 16 x 0 249 x 1 16 It is important to remember that coefficients for unlike pairs must be multiplied by two Note that the list of values is allowed to span more than one line Also note that you can provide coefficients in fm rather than 10 28 m as shown here as long as your data are similarly scaled 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 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 block of data keywords where required you might not bother for the data sets using the natural isotopes 4 3 Using experimental data One unfortunate aspect of the world of total scattering is that different c
215. shell command convert transparent black lt name gt ppm lt name gt lt extension gt 2Note that the mathematics community switches the meanings of these symbols here 0 gives the angle a vector makes with the axis 0 lt 0 lt 1809 and gives the angle that the vector is rotated about the axis 0 lt lt 3609 13The PPM format is described at http en wikipedia org wiki Portable_pixmap which is available from http www imagemagick org 64 154 RMCProfile Manual v6 5 2 4 7 USING POTENTIALS 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 OS X and Adobe s Photoshop are able to read and manipulate files in the PPM format 4 7 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 his togram file to a PPM file This gives the user some co
216. son running the simulation or experiment This is designed for your future benefit This is used for metadata and is not compulsory KEYWORDS Requires text that act as keywords for your pos sible future benefit This is used for metadata and is not compulsory MAGNETISM 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 MATERIAL Requires text to act as a title for the material being studied This is used for metadata and is not compulsory MAXIMUM MOVES Requires values of the maximum move of each atom Currently the units are not interpreted default units are Angstroms 36 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE MINIMUM_DISTANCES Requires numbers of the minimum approach distances between pairs of atoms Default val ues are zero if this keyword is not provided Cur rently the units are not interpreted default units are ngstroms 2 EUTRON_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 10 30 m The default values calculated by the code if this keyword is not given It can be overwritten within the neutron data block of subordinate keywords see tion 4
217. st and the number of atoms of each type This would have the form summon t atoms t numbers of species c rmcprofile config 6 300k xml Another usage might be 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 summon t r t partial2 t partial3 c rmcprofile config 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 summon t numbers of species rmcprofile config ag3cocn6_300k xml 112 154 Manual v6 5 2 6 3 CML BASED ANALYSIS TOOLS might return numbers_of_species 864 288 1728 17281 This might not be least 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 W
218. t 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 83 154 RMCProfile Manual v6 5 2 4 14 RMCPROFILE VERSION 3 FILES 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 Symbol for second atom use spaces to 1 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 12 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 nearest 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 hist
219. ta 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 methane braggout Will contain the calculated and experimental Bragg diffraction data methane bragg csv will contain the calculated and experimental Bragg diffraction data in CSV format methane cssr Which contains the configuration in a form that can be read by several visualisation programs including CrystalMaker which is endorsed by the authors 2Comma 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 31 154 RMCProfile Manual v6 5 2 3 4 OUTPUT FILES hkls contains information used by the Bragg modules and which be retained to be used by a subsequent run of RMCProfile methane amp contains information used by the Bragg modules and which can be retained to be used by a subsequent run of RMCProfile methane ylm contains lists of the mean bond spherical harmonics and Kubic harmonics These files will be described in subsequent chapters 32 154 RMCProfile Manual v6 5 2 CHAPTER 4 INPUT FILES Chapter 4 Input Files 41 RMCProfile main data file 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
220. te 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 10 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 dat file and poly sio and osi files supplied The 1 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 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 6 1 4 10 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 TiOsSr In this way the same constraint be used to study Ca Sr _ TiO3 or any similar system To use this restr
221. ted until its Fourier transform is consistent with the experimental data It is possible to include the effects of resolution when comparing the computed Fourier transform with the experimental data so the effects of resolution are automatically removed from the process The effect of ignoring resolution is easy to understand The experimental data represents the convolution of the actual scattering function with the function describing the resolution Thus the Fourier transform will be the product of the PDF and the Fourier transform of the resolution function which typically will be a function peaked at 0 and decaying slowing with r Thus the features at higher r will be damped and the important error introduced into the analysis will be that the coordination numbers represented by the data will be lower than the true coordination numbers This is likely to lead to the RMC method introducing some additional disorder into the models it produces 10 154 Manual v6 5 2 2 3 FITTING THE BRAGG PROFILE Users need to be aware that the PDF is weighted by the strength of scattering from individual atoms in addition to a weighting by the relative concentration of each atom In the case of neutron scattering this weighting will correspond to the product of scattering lengths of the two atoms for each contribution to the PDF In the case of x ray scattering there is a complicating factor that the effects of the size of atoms are appr
222. tem and then modify this as you need to At this point it is worth bringing to your attention that 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 it may eventually become impossible to maintain the code in this format Hence we do recommend using the version 6 files and methods if they meet your needs 4 44 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 restraints available with different combinations of polyhedra For the full list of options and the files required please see the polyhedral restraints section below The sf and s 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 4 10 4 15 Tools to upgrade from use of classic and RMCA versions At this point in the development of the RMCProfile code we cannot guarantee that all functionality is compatible with the classic version and we strongly recommend making the switch to Version 6 To make this easier we have provided some tools to help you upgrade There are basically two things you have to change First is the dat file a
223. 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 intramolec ular 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 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 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 jobs To switch will only take you a few minutes time that you will more than recoup once your job has run 87 154 RMCProfile Manual v6 5 2 CHAPTER 5 EXAMPLES Chapter 5 Examples 51 Example of using total scattering data 511 Neutron total scattering data file We consider here an RMC study of KCN in its disordered phase This has a very simple crystal structure based on the textbook NaCl structure with the CN molecular anion having disordered orientations In this case we are using a merged file for the total scattering data The start of the file
224. 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 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 34 154 RMCProfile Manual v6 5 2 41 3 Major keywords 4 1 RMCPROFILE MAIN DATA FILE 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 ATOMS AVE RAG COORD BRAGG BVS CML COMMENT NATION_CONSTRAINTS DATA FILE VE
225. 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 6 1 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 example 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 6 1 6 get gsas bragg This program used to be required to extract the information required by RMCProfile a GSAS refinement to enable the Bragg profile to be fitted but the same functionality is now be provided by data2config 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 re quires at least the 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 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 hk1 and inst files If the GSAS executable are
226. 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 A 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 to give 6 where the first term will describe pairs of atoms and will be considered more detail below where is the proportion of atoms of type m 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 115 154 RMCProfile Manual v6 5 2 1 1 TOTAL SCATTERING a is 8 sin Qr 26 dr A 7 where the new function G r describes the distribution of interatomic distances G r CmCnbmDn gmn r 1 8 m n and is the number of atoms of any type per unit v
227. thod the experimental total scattering data corresponding to the values of y in the equation for 2 can D r 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 in the following form 22 where Sm 0 1 and we define a separate X for each set of data 118 154 RMCProfile Manual v6 5 2 1 3 RMC METHOD Ld Qj Qlexp Q x 02 0 23 Xbp 24 XSrofile LE fie 6 25 Y 1 26 XBs oplat o A 27 XB 6050 cos 6 A 28 The term corresponds to the polyhedral constraints Keen 1997 1998 where may 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 20026 The terms x amp s and 2 the new molecular constraints where the parameters designed to be realistic so that the weighting term is now related to the experiment temperature The function profiie t describes the Bragg diffraction pattern Our work is mostly based on time of flight neutron sources so prorie f a function of neutr
228. tic structures A reasonable general approach appears to attempt refinement of the nuclear struc ture 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 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 The value entered as the input parameter MAx SP IN MOVEMENT is the variable 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 peri odic 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 2 10 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
229. ting triplets file then rename or delete it The structure of this file is important 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 The lt snip gt lines replace similar data removed for the sake of brevity 62 154 Manual v6 5 2 4 7 USING POTENTIALS 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 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 Zn 1 2 101 C 102 C 101 103 101 C 104 C 101 105 C 4 Zn 1 0 The first line describes the connectivity when the atom Zn in this case is 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
230. tructure 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 Write a diagnostics file it isn t worth reading because there is lot of duplicate data but is useful if you have problems dlpoly Write DLPOLY file you get this conversion for free because it was easy to implement help Provides help information to the computer terminal window 100 154 RMCProfile Manual v6 5 2 6 1 DATA PREPARATION TOOLS Produces configuration that is a single unit cell from the provided struc ture Order the atoms as list supplied response to a question output This will tell the program to write all output files to a directory folder sup plied as an argument immediately following this flag metadata Allows metadata to be supplied in a file whose name is provided as an argument to this flag The metadata file containing keyword value pairs fol lowing a heading line containing the single word metadata case inde pendent square brackets required and with one metadata item provided per line with keyword and value separated by an sign Allowed
231. uce an animated gif We will do this quickly here by editing the file spinplot in changing the last entry from to T This part of the file is a that instructs the program to prepare a series of views that can be assembled to form an animation Re running the command Spinplot spinplot in will now give a series of 24 files numbered 01 mno spins ppmto 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 magnons from the sharpness of the peaks in these correlation functions 22 154 RMCProfile Manual v6 5 2 2 11 FITTING EXAFS DATA 2 11 Fitting EXAFS data We are working to incorporate documentation of the EXAFS part of RMCProfile into this man ual In the meantime please refer to the EXAFS manual at http www rmcprofile org imagesFhj 5 51 Rmcprofile exafs manual pdf for more information 2 12 Producing starting configurations 2 12 1 Introduction The RMC method is designed to work with atomic configurations that contain of order of a few thousand to a few tens of thousands of atoms with
232. uired that mktemp is installed on the comput ing running the code Default is not to perform this action 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 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 OUTPUT CONFIGURATION Instructs the code to write the configuration into a CML file Default is to write to a standard configuration file not yet implemented DISTANCE WINDOW 41 154 RMCProfile Manual v6 5 2 4 1 RMCPROFILE MAIN DATA FILE gt MNDIST Give the closest approach distances for each atom pair These are ordered as the partials so 2 atom configuration three distances would be given for pair 1 1 pair 1 2 and pair 2 2 respectively gt MXDIST Exactly the same as the previous keyword but this time giving the furthest away distances FIXED_COORDINATION_CONSTRAINTS gt CSTR Give in order the following parameters central atom type e g 1 neighbour atom type e g 2 the dis tances between which to calculate the coordination number e g 0 2 0 the desired coordination number e g 4 the fraction of
233. um Using the bond valence sum BVS constraint requires the block of keywords as described in section 4 1 2 Here is an example of setting up this constraint for the system yttria stabilized zirconia 2702 20 BVS gt Y Zr OXID 3 4 2 WEIGHTS 0 055 0 055 0 140 gt RIJ 0 2 019 1 928 BVAL 0 0 37 0 37 CUTOFF 3 2 3 2 gt 400000 gt 200000 This should be fairly self explanatory but it is worth drawing attention to the gt OXID line which contains the oxidation states of each constituent atom and to the RIJ line which contains the bond valence parameters for each atom pair zeroes for non bonded pairs These values can be found tabulated in Appendix 3 1 and are taken from Brese and O Keefe Acta Cryst B 47 192 197 1991 94 154 RMCProfile Manual v6 5 2 5 6 EXAMPLE OF USING CONSTRAINTS The order in which the parameters are given is very important and slightly different to how the partials and coefficients are ordered elsewhere For BVS you do not include like atom pairs Configuration Number of pairs Order AB 1 AB ABC 3 AB AC BC ABCD 6 AB AC AD BC BD CD ABCDE 10 AB AC AD AE BC BD BE CD CE DE The current maximum number of atom types is 10 5 6 Example of using constraints 5 6 1 Distance window A good example of the use of distance window constraints would be the wor
234. umber density line is also not required but will be written by RMCProfile in sub sequent writes of the configuration file 11 Ang deg lineis 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 prece dence Both will be generated in subsequent writes of the configuration file 76 154 RMCProfile Manual v6 5 2 4 11 RMC VERSION 6 FORMAT CONFIGURATION FILES 8 The Lattice vectors line and the following three lines containing the vectors describing the shape and dimensions of the configuration These lines are not required if 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 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 s
235. used for any system with the same polyhedral connectivity It is important to note 14 154 Manual v6 5 2 2 10 MAGNETIC STRUCTURE MODELLING that the polyhedral restraints are not compatible with the atom swapping ability of RMCProfile and therefore you will need to use the distance window constraint see section 2 4 to maintain the connectivity of a system in which they wish to investigate swapping One can envisage the application of these restraints in a system such as zeolitic SiOz polymorph wherein the SiOz restraint can hold the tetrahedra together thus allowing RMCP rofile to concen trate on the structural features of more interest to the experimenter 2 10 Magnetic structure modelling Some of this section refers to features in older versions of RMCProfile and as such is in need of updating We hope to have an updated version ready for the next release In the meantime please refer to the information below and get in touch if you have any questions about the implementation of magnetism in RMCProfile 2 10 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 the spin configuration are then determined by the positions in the atomistic uration Each RMC move involves either a change in atomic positions or magnetic moment ori e
236. v6 5 2 4 4 USING MAGNETISM 4 4 Using magnetism You may wish to include magnetism in your refinement for several reasons Firstly you may wish to find out more about the magnetic structure of your material and allow a greater degree of freedom than other techniques may allow Alternatively you may be mainly interested in the nuclear structure of your material and include the magnetism just to ensure that the relevant peaks in your data are properly fitted Finally you might be interested in both the positions of the atoms and their magnetic moments RMCProfile should be able to help you in each of these cases just choose what aspects of your structure you wish to refine A couple of caveats regarding the use of magnetism in your refinements which may be obvious Firstly the magnetic scattering is only included for neutron data sets so don t expect the magnetic contribution to appear in x ray data refinements Secondly magnetic correlations are not included in any fits to PDF data because of complications that arise when Fourier transforming magnetic data The other side to this is that if you transform your experimental data into real space there will be contributions from both the nuclear and magnetic scattering which can make accurate fitting difficult In some cases it may be best to avoid the use of real space functions if the magnetic scattering cannot be separated from the nuclear component 441 The data file RMC
237. w 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 109 154 RMCProfile Manual v6 5 2 6 3 CML BASED ANALYSIS TOOLS Sample screen shots are shown in Figures 6 1 and 6 2 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 experts our view is that output files should not need to be read hand in hand with the manual to make sense of them is supplied with the RMCProfile v6 package It does not need to be installed 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 6 3
238. y double clicking on the RMCProfile setup command file This should bring up a terminal window called RMCProfile version 6 28 154 RMCProfile Manual v6 5 2 3 2 SETTING UP THE FILES FOR AN RMCPROFILE CALCULATION To install RMCProfile on Linux machine 1 Download the file that fits your system i e 32 or 64 bit 2 Put the file in your top directory once it has downloaded 3 Type tar pxvzf rmcprofile package_v6_5_1_linux_32 tgz change 32 to 64 if you have that version This will unpack everything into RMCProfile package directory 4 To run the program cd to the RMCProfile package directory and type RMCProfile setup and hit return This should bring up an xterm window called RMCProfile version 6 There are various other programs supplied as tools to help with preparation and analysis of the RMCProfile 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 3 2 Setting up the files for an RMCProfile calculation RMCProfile requires a number of input files that are described in more detail in the following sections but are listed here both to give a quick overview and also to act as a handy checklist In short the input files are the file containing main control data dat one file containing the starting configuration rmc6f his6f
239. ymbol 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 one of the real elements You are allowed to use for deuterium and you can use va for a vacant 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 2 values range from 0 1 single optional integer that is appropriate if the configuration is supercell of 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 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 supercel
240. 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 contains 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 Most of these neighbour files should be generated using the neighbour list program supplied with RMCProfile and described in section 6 1 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 10 14 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 and cf and fc files supplied The 1 file contains title line which is ignored and the next line must contain the ideal 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 file c

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