ADVANCED USERS DMACRYS & NEIGHCRYS manual Manual ...

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diff.(abs) => 0.0215 -0.0439 0.0167 0.0000 0.0000 0.0000 diff.(%) => 0.2176 -0.4335 0.2382 0.0000 0.0000 0.0000 Cell Volume ( Cubic Angstroms ) Cell density ( g/cubic cm) Initial => 700.0617 1.0639 Final => 700.2082 1.0636 diff.(abs) => 0.1465 -0.0002 diff.(%) => 0.0209 -0.0209 Dipole per unit cell in global axis system (eA) x y z total dipole Initial : 0.0000000 0.0000000 0.0000000 0.0000000 Final : 0.0000000 0.0000000 0.0000000 0.0000000 Printed output Initial crystalographic positions of molecule centres of mass Molecule a-vectors b-vectors c-vectors MOLWCH XTLCOM(JJJ),JJJ=1,3 Final crystalographic positions of molecule centres of mass Molecule a-vectors b-vectors c-vectors MOLWCH XTLCOM(JJJ),JJJ=1,3 The changes to the positions of the molecules’ centres of mass are printed out. Example output Initial crystalographic positions of molecule centres of mass Molecule a-vectors b-vectors c-vectors 1 0.896521 0.156371 0.107545 2 0.396521 0.343629 0.892455 3 0.103479 0.656371 0.392455 4 0.603479 0.843629 0.607545 5 0.103479 0.843629 0.892455 6 0.603479 0.656371 0.107545 7 0.896521 0.343629 0.607545 8 0.396521 0.156371 0.392455 Final crystalographic positions of molecule centres of mass Molecule a-vectors b-vectors c-vectors 1 0.896612 0.156875 0.107227 2 0.396612 0.343125 0.892773 3 0.103388 0.656875 0.392773 4 0.603388 0.843125 0.607227 5 0.103388 0.843125 0.892773 6 0.603388 0.656875 0.107227 7 0.896612 0.343125 0.607227 8 0.396612 0.156875 0.392773 Printed output Direction cosines between axes before and after program run for molecule MOLWCH new axis old axis || X Y Z // LABAX(IAXIS) (DIRCOS(IAXIS,JAXIS),JAXIS=1,3) LABAX(IAXIS) (DIRCOS(IAXIS,JAXIS),JAXIS=1,3) LABAX(IAXIS) (DIRCOS(IAXIS,JAXIS),JAXIS=1,3) Actual angles between axes (Degrees): new axis old axis || X Y Z // LABAX(IAXIS) RADDEG*ACOS(DIRCOS(IAXIS,JAXIS)),JAXIS=1,3 LABAX(IAXIS) RADDEG*ACOS(DIRCOS(IAXIS,JAXIS)),JAXIS=1,3 LABAX(IAXIS) RADDEG*ACOS(DIRCOS(IAXIS,JAXIS)),JAXIS=1,3 Euler (y-convention) angles of new system in old: 38
first rotation about z Phi = RADDEG* PHI first rotation about y Theta= RADDEG*THETA second rotation about z Psi = RADDEG*PSI Equivalent to a single rotation of RADDEG*ACTANG degrees around the global axis vector: RNORM(JJJ),JJJ=1,3 [local axis {orig. system} vector: 0.503410 -0.802287 0.320802 ] The changes to the positions of the molecular axes are printed out for each molecule. Example output Direction cosines between axes before and after program run for molecule 1 new axis old axis || X Y Z // X 0.999983 -.005195 -.002827 Y 0.005186 0.999981 -.003228 Z 0.002844 0.003213 0.999991 Actual angles between axes (Degrees): new axis old axis || X Y Z // X 0.338852 90.297633 90.161972 Y 89.702890 0.349966 90.184935 Z 89.837070 89.815908 0.245838 Euler (y-convention) angles of new system in old: first rotation about z Phi = 131.510288 first rotation about y Theta= 0.245838 second rotation about z Psi = -131.212915 Equivalent to a single rotation of 0.385832 degrees around the global axis vector: 0.478225 -0.421043 0.770729 [local axis {orig. system} vector: 0.503410 -0.802287 0.320802 ] Printed output Molecular movement including strains (Angstroms) Mol. | Dx | III DELXML(III) RMS Aver. RMS aver The molecular movement for each molecule is printed out. Example output Molecular movement including strains (Angstroms) Mol. | Dx | 1 0.020221 2 0.028084 3 0.025366 4 0.044559 5 0.045521 6 0.026652 7 0.029589 8 0.012985 RMS Aver. 0.030930 Printed output Figure of shame as defined in Acta Cryst. B49 868 1993. in our case RMS values are used to take the place of symmetry independent factors so | |2 | |2 | |2 F = |0.5 RMS D THETA | + | 10 RMS Dx | + SUM (d=a,b,c) | 100 Dd | | | | | | | 2 39
Page 1 and 2: ADVANCED USERS DMACRYS manual Manua
Page 3 and 4: 1 INTRODUCTION This document descri
Page 5 and 6: SPLI ACCM is usually set to equal C
Page 7 and 8: LATT BASI Digit 3 Digit 4 Digit 5 0
Page 9 and 10: CCLS 17 FORMATTED WRITE Output clos
Page 11 and 12: The ACCTH operand is retained for f
Page 13 and 14: H_F1_1_____ would be the short atom
Page 15 and 16: Two basis atoms have been found at
Page 17 and 18: The directive order for the initial
Page 19 and 20: POTENTIAL BETWEEN SPECIES JSPECA AN
Page 21 and 22: BUCK BrBR BrBR 2662.410975 0.330736
Page 23 and 24: Operand types Operand names F CUTMO
Page 25 and 26: NNCU C_ C_ 1.600 C_ O_ 1.400 C_ H_
Page 27 and 28: Molecule No. Centred at Total Mass
Page 29 and 30: Operand Type Operand Name A WKEY WC
Page 31 and 32: Maximum number of iterations = 1000
Page 33 and 34: | | R => R + | 1/2 E E 1/2 E | R |
Page 35 and 36: If ABS(GD2/GD1) is greater than 0.2
Page 37 and 38: Contributions to inter-molecular el
Page 39: Printed output Final molecular cent
Page 43 and 44: Example output Sorted displacements
Page 45 and 46: • The forces and torques are also
Page 47 and 48: upper and lower bounds. However, si
Page 49 and 50: Appendix A. Full list of all direct
Page 51 and 52: Appendix B. Options for printed out
Page 53 and 54: The exponent N is read in from the
Page 55 and 56: C = C r a RMAX Error messages ERROR
Page 57 and 58: K R0 D*Q1*Q2 RMIN RMAX K R0 D*Q1 *Q
Page 59 and 60: The polynomials are fitted so that
Page 61 and 62: 9 10 11 9 12 13 14 H···H H bonde
Page 63 and 64: Appendix E. Possible control parame
Page 65 and 66: a 1 L 0 0 b 0 1 0 c 0 0 1 Multiply

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