HEADER NiSe2 Pyrit (Acta Chem. Scand.
v. 23 p. 2325 1969)
VERS LMASA-47
STRUC ALAT=11.2683
PLAT=1 0 0
0 1 0
0 0 1
CLASS ATOM=NI Z=28
ATOM=Se Z=34
SITE ATOM=NI POS= .0 .0 .0
ATOM=NI POS= .5 .0 .5
ATOM=NI POS= .0 .5 .5
ATOM=NI POS= .5 .5 .0
ATOM=Se POS= .383 .383 .383
ATOM=Se POS= .617 .617 .617
ATOM=Se POS= .117 .617 .883
ATOM=Se POS= .883 .383 .117
ATOM=Se POS= .617 .883 .117
ATOM=Se POS= .383 .117 .883
ATOM=Se POS= .883 .117 .617
ATOM=Se POS= .117 .883 .383
The input consists of tokens, like ATOM= or Z=. These are grouped together in categories, like CLASS. The name of a category always starts in the first column of a line. This will be explained in detail in Section V. ALAT= is a lattice constant in a.u. (i.e. Bohr radii), PLAT= are the lattice translation vectors and POS= are the atomic positions. The latter two are in Cartesian coordinates and in units of ALAT.
All Ni atoms and all Se atoms are equivalent i.e. there are two classes. From the information in the CTRL file, the program will find the symmetry i.e. all space group operations and the generators of the space group. If the symmetry of the bravais lattice is incompatible with the symmetry of the basis, then the symmetry of the bravais lattice is used. Alternatively to the CTRL file above, the symmetry generators and only one of each of the inequivalent atoms could have been given. The program will complete the basis:
HEADER NiSe2 Pyrit (Acta Chem. Scand.
v. 23 p. 2325 1969)
VERS LMASA-47
STRUC ALAT=11.2683
PLAT=1 0 0
0 1 0
0 0 1
CLASS ATOM=NI Z=28
ATOM=Se Z=34
SITE ATOM=NI POS= .0 .0 .0
ATOM=Se POS= .383 .383 .383
SYMGRP NGEN=3 GENGRP=I R3D MX:(.5,.5,0)
The category SYMGRP contains three tokens: NGEN= the number of
generators supplied,
GENGRP= the names of the generators as defined in
the Subsection `Category SYMGRP'.
A third possibility is to use the interactive program lminit.run in the main directory. An example is shown below, where the user's answer to the query is indicated by the string after `->' and followed by `(Answer)'.
| QUERY : SPCGRP:
| SYMBOL OR NUMBER OF SPACE GROUP
|
| Enter: 'nnn', nnn is the value for SPCGRP,
| 'a' to abort program execution.
| ->205 (Answer)
Space group: Pa-3 No.:205
Crystal system: cubic
Generators: I R3D MX::(1/2,1/2,0)
| QUERY : atomic-units ? (else in Angstrom)
|
| Enter: 'nnn', nnn is the value for ATUNITS,
| default value=T
| 'a' to abort program execution.
| '/' to accept default value
| ->/
Now enter lattice parameters
| QUERY : A:lattice constant (atomic units)
|
| Enter: 'nnn', nnn is the value for A,
| 'a' to abort program execution.
| ->11.2683 (Answer)
CTRLUC: PLAT ALAT=11.2683
1.00000 .00000 .00000
.00000 1.00000 .00000
.00000 .00000 1.00000
| QUERY: label or nuclear charge of class 1
|
| Enter: 'nnn', nnn is the value for label,
| 'a' to abort program execution.
| 'q' to quit
| ->28 (Answer)
Class: Ni ; nuclear charge 28 (atom Ni)
| QUERY: X = position of Ni (in units of the
| translation vectors a, b, c)
|
| Enter: 'nnn', nnn is the value for X,
| default value=0. 0. 0.
| 'a' to abort program execution.
| '/' to accept default value
| ->/ (Answer)
| QUERY: label or nuclear charge of class 2
|
| Enter: 'nnn', nnn is the value for label,
| 'a' to abort program execution.
| 'q' to quit
| ->34 (Answer)
Class: Se ; nuclear charge 34 (atom Se)
| QUERY : X = position of Se
|
| Enter: 'nnn', nnn is the value for X,
| default value=0. 0. 0.
| 'a' to abort program execution.
| '/' to accept default value
| ->.383 .383 .383
| QUERY: label or nuclear charge of class 3
|
| Enter: 'nnn', nnn is the value for label,
| 'a' to abort program execution.
| 'q' to quit
| ->q (Answer)
CHKSYM: Check the symmetry of the crystal:
GENGRP: A subgroup of the space group will
be created from 3 generators
The generators created 24 sym. ops.
ADDBAS: The basis has been extended from
2 to 12 atoms.
The new positions are:
ATOM=Ni POS= .500 .500 .000
ATOM=Ni POS= .000 .500 .500
ATOM=Ni POS= .500 .000 .500
ATOM=Se POS= -.383 -.383 -.383
ATOM=Se POS= .117 .883 .383
ATOM=Se POS= .883 .117 -.383
ATOM=Se POS= .383 .117 .883
ATOM=Se POS= .883 .383 .117
ATOM=Se POS= -.383 .883 .117
ATOM=Se POS= .117 -.383 .883
SYMLAT: lattice invariant under 48 sym. ops.
SYMCRY: crystal invariant under 24 sym. ops.
SHOSYM: Bravais system : cubic
Bravais lattice: cubic primitive
Centring type : P
Crystal family : cubic
Crystal system : cubic
Point group : m-3
The resulting CTRL file looks like this:
HEADER Ni4Se8, cubic primitive
SYMGRP NGEN=3 GENGRP=I R3D MX:(.5,.5,0)
SPCGRP=Pa-3
STRUC ALAT=11.2683
PLAT=1 0 0
0 1 0
0 0 1
CLASS ATOM=Ni Z=28
ATOM=Se Z=34
SITE ATOM=Ni POS=0.000 0.000 0.000
ATOM=Ni POS=0.500 0.500 0.000
ATOM=Ni POS=0.500 0.000 0.500
ATOM=Ni POS=0.000 0.500 0.500
ATOM=Se POS=0.383 0.117 -.117
ATOM=Se POS=-.383 -.117 0.117
ATOM=Se POS=-.117 0.383 0.117
ATOM=Se POS=0.117 -.383 -.117
ATOM=Se POS=0.117 -.117 0.383
ATOM=Se POS=-.117 0.117 -.383
ATOM=Se POS=0.383 0.383 0.383
ATOM=Se POS=-.383 -.383 -.383HEADER Ni4Se8, cubic primitive
VERS LMASA-47
IO VERBOS=30 OUTPUT=LM ERR=ERR
SYMGRP NGEN=3 GENGRP=I R3D MX:(.5,.5,0)
SPCGRP=Pa-3
STRUC ALAT=11.2683
PLAT=1 0 0
0 1 0
0 0 1
DIM NBAS=12 NCLASS=2 NL=3 LDIM=68
IDIM=40 NSYMOP=24
CLASS ATOM=Ni Z=28 R=2.41776510
ATOM=Se Z=34 R=2.28352037
SITE ATOM=Ni POS=0.000 0.000 0.000
ATOM=Ni POS=0.500 0.500 0.000
ATOM=Ni POS=0.500 0.000 0.500
ATOM=Ni POS=0.000 0.500 0.500
ATOM=Se POS=0.383 0.117 -.117
ATOM=Se POS=-.383 -.117 0.117
ATOM=Se POS=-.117 0.383 0.117
ATOM=Se POS=0.117 -.383 -.117
ATOM=Se POS=0.117 -.117 0.383
ATOM=Se POS=-.117 0.117 -.383
ATOM=Se POS=0.383 0.383 0.383
ATOM=Se POS=-.383 -.383 -.383
The two tokens (R=) with the MT-radii in a.u. have been inserted in category CLASS. Furthermore, a new class, IO, has been inserted with the tokens: VERBOS= which specifies the amount of output the programs print and the number of default tokens which will be inserted in the CTRL file by the programs which updates the CTRL file, OUTPUT= which gives a file name to which standard out will be directed, ERR= which gives a file name to which error messages will be directed.
Info: impossible to reach VOL, increase OMMAX. CELL VOLUME= 1430.78771, SUM OF SPHERE VOLUMES= 992.45473 IB JB CL1 CL2 DIST SUMRS 1/d 1/s1 1/s2 ========================================== 1 5 Ni Se .42 .48 16 27 28 ------------------------------------------ 5 1 Se Ni .42 .48 16 28 27 5 6 Se Se .41 .47 16 28 28 ------------------------------------------
The first line tells that space filling could not be reached with the default maximum overlaps (two atomic spheres are allowed to overlap no more than 16% in the sence of 1/d below, max. overlap between an atomic and an interstitial sphere is 18%, and max. overlap between two interstitial spheres is 20%).
The next two lines show the cell volume and the volume inside the expanded spheres.
In the table,
each line displays two neighboring atoms with WS-radii s1 and s2, and
the distance between them d. Under `1/d', `1/s1', and `1/s2' are the
results of
,
, and
, respectively, in percent.
If the two sphere radii are very much different, one should check
`1/s1', where s1 is the smallest radius. (A big sphere may swallow a
small sphere.)
Since in the present case space filling could not be reached, interstitial spheres have to be inserted.
HEADER Ni4Se8, cubic primitive
VERS LMASA-47
IO VERBOS=30 OUTPUT=OVL ERR=ERR
SYMGRP NGEN=3 GENGRP=I R3D MX:(.5,.5,0)
SPCGRP=Pa-3
STRUC ALAT=11.2683
PLAT=1 0 0
0 1 0
0 0 1
DIM NBAS=36 NCLASS=3 NL=3 LDIM=68
IDIM=40 NSYMOP=24
CLASS ATOM=Ni Z=28 R=2.41776510
ATOM=Se Z=34 R=2.28352037
ATOM=E Z= 0 R=1.53150056
SITE ATOM=Ni POS=0.00000 0.00000 0.00000
ATOM=Ni POS=0.50000 0.50000 0.00000
ATOM=Ni POS=0.50000 0.00000 0.50000
ATOM=Ni POS=0.00000 0.50000 0.50000
ATOM=Se POS=0.38300 0.11700 -.11700
ATOM=Se POS=-.38300 -.11700 0.11700
ATOM=Se POS=-.11700 0.38300 0.11700
ATOM=Se POS=0.11700 -.38300 -.11700
ATOM=Se POS=0.11700 -.11700 0.38300
ATOM=Se POS=-.11700 0.11700 -.38300
ATOM=Se POS=0.38300 0.38300 0.38300
ATOM=Se POS=-.38300 -.38300 -.38300
ATOM=E POS=0.28510 -.18060 0.09608
ATOM=E POS=-.28510 0.18060 -.09608
ATOM=E POS=0.09608 0.28510 -.18060
ATOM=E POS=-.09608 -.28510 0.18060
ATOM=E POS=0.18060 -.09608 -.28510
ATOM=E POS=-.18060 0.09608 0.28510
ATOM=E POS=0.31939 0.09608 0.21489
ATOM=E POS=0.21489 0.31939 0.09608
ATOM=E POS=-.31939 -.09608 -.21489
ATOM=E POS=-.21489 -.31939 -.09608
ATOM=E POS=0.09608 0.21489 0.31939
ATOM=E POS=-.09608 -.21489 -.31939
ATOM=E POS=0.40391 -.21489 -.18060
ATOM=E POS=-.40391 0.21489 0.18060
ATOM=E POS=-.18060 0.40391 -.21489
ATOM=E POS=0.18060 -.40391 0.21489
ATOM=E POS=0.21489 0.18060 -.40391
ATOM=E POS=-.21489 -.18060 0.40391
ATOM=E POS=0.40391 -.28510 0.31939
ATOM=E POS=0.31939 0.40391 -.28510
ATOM=E POS=-.40391 0.28510 -.31939
ATOM=E POS=-.31939 -.40391 0.28510
ATOM=E POS=-.28510 0.31939 0.40391
ATOM=E POS=0.28510 -.31939 -.40391
The program found 24 interstitial spheres, all equivalent, with a sphere radius between 0.9 and 4.0 a.u. These limits are default and can be changed. Notice that a new category DIM has been inserted, which contain information about some dimensions.
IB JB CL1 CL2 DIST SUMRS 1/d 1/s1 1/s2 ========================================= 1 5 NI Se .42 .47 13 22 23 1 20 NI E1 .35 .40 13 18 29 ----------------------------------------- 5 1 Se NI .42 .47 13 23 22 5 6 Se Se .41 .46 13 23 23 5 14 Se E1 .34 .38 13 19 28 5 15 Se E1 .38 .38 1 1 2 5 17 Se E1 .34 .38 13 19 28 5 22 Se E1 .34 .38 13 19 28 5 23 Se E1 .34 .38 13 19 28 5 29 Se E1 .38 .38 1 1 2 5 31 Se E1 .34 .38 13 19 28 5 34 Se E1 .34 .38 13 19 28 5 35 Se E1 .38 .38 1 1 2 5 36 Se E1 .34 .38 13 19 28 ----------------------------------------- 13 2 E1 NI .35 .40 13 29 18 13 6 E1 Se .34 .38 13 28 19 13 7 E1 Se .38 .38 1 2 1 13 8 E1 Se .34 .38 13 28 19 13 12 E1 Se .34 .38 13 28 19 13 15 E1 E1 .27 .31 12 21 21 13 25 E1 E1 .30 .31 1 2 2 -----------------------------------------
The program found space filling with a maximum overlap of 13% which is fine and one can proceed.
HEADER Ni4Se8, cubic primitive
VERS LMASA-47
IO VERBOS=50 HELP=F WKP=F IACTIV=F
ERRTOL=2 OUTPUT=CTL ERR=ERR
SYMGRP NGEN=3 GENGRP=I R3D MX:(.5,.5,0)
SPCGRP=Pa-3 USESYM=F
STRUC ALAT=11.2683
PLAT=1 0 0
0 1 0
0 0 1 FIXLAT=T
DIM NBAS=36 NCLASS=3 NL=3 LDIM=92
IDIM=232 NSYMOP=24 NKP=11
OPTIONS NSPIN=1 REL=T CCOR=T NONLOC=F
NRXC=1 NRMIX=2 CORDRD=F
NITATOM=30 CHARGE=F FATBAND=F AFM=F
FS=F CARTESIAN=T WRIBAS=F Q=----
CLASS ATOM=Ni Z=28 R=2.72719158 LMX=2
CONF=4 4 3 4 IDXDN=1 1 1 IDMOD=0 0 0
ATOM=Se Z=34 R=2.57576616 LMX=2
CONF=4 4 4 4 IDXDN=1 1 2 IDMOD=0 0 0
ATOM=E Z= 0 R=1.72750257 LMX=2
CONF=1 2 3 4 IDXDN=1 2 2 IDMOD=0 0 0
SITE ATOM=Ni POS=0.00000 0.00000 0.0000
ATOM=Ni POS=0.50000 0.50000 0.0000
ATOM=Ni POS=0.50000 0.00000 0.5000
ATOM=Ni POS=0.00000 0.50000 0.5000
ATOM=Se POS=0.38300 0.11700 -.1170
ATOM=Se POS=-.38300 -.11700 0.1170
ATOM=Se POS=-.11700 0.38300 0.1170
ATOM=Se POS=0.11700 -.38300 -.1170
ATOM=Se POS=0.11700 -.11700 0.3830
ATOM=Se POS=-.11700 0.11700 -.3830
ATOM=Se POS=0.38300 0.38300 0.3830
ATOM=Se POS=-.38300 -.38300 -.3830
ATOM=E POS=0.28510 -.18060 0.0960
ATOM=E POS=-.28510 0.18060 -.0960
ATOM=E POS=0.09608 0.28510 -.1806
ATOM=E POS=-.09608 -.28510 0.1806
ATOM=E POS=0.18060 -.09608 -.2851
ATOM=E POS=-.18060 0.09608 0.2851
ATOM=E POS=0.31939 0.09608 0.2148
ATOM=E POS=0.21489 0.31939 0.0960
ATOM=E POS=-.31939 -.09608 -.2148
ATOM=E POS=-.21489 -.31939 -.0960
ATOM=E POS=0.09608 0.21489 0.3193
ATOM=E POS=-.09608 -.21489 -.3193
ATOM=E POS=0.40391 -.21489 -.1806
ATOM=E POS=-.40391 0.21489 0.1806
ATOM=E POS=-.18060 0.40391 -.2148
ATOM=E POS=0.18060 -.40391 0.2148
ATOM=E POS=0.21489 0.18060 -.4039
ATOM=E POS=-.21489 -.18060 0.4039
ATOM=E POS=0.40391 -.28510 0.3193
ATOM=E POS=0.31939 0.40391 -.2851
ATOM=E POS=-.40391 0.28510 -.3193
ATOM=E POS=-.31939 -.40391 0.2851
ATOM=E POS=-.28510 0.31939 0.4039
ATOM=E POS=0.28510 -.31939 -.4039
SCALE SCLWSR=T OMMAX1=.16 .18 .20
OMMAX2=.40 .45 .50
STR KAPPA2=0 RMAXS=3.2 NDIMIN=350
NOCALC=F IALPHA=0
DOWATS=F DELTR=.1 LMAXW=8
ATOM=Ni SIGMA=.7 .7 .7
ATOM=Se SIGMA=.7 .7 .7
ATOM=E SIGMA=.7 .7 .7
START NIT=30 BROY=T WC=-1 NMIX=1 BETA=.5
FREE=F CNVG=.00001 CNVGET=.00001
BEGMOM=T CNTROL=T
EFERMI=-.25 VMTZ=-.75
ATOM=Ni P=4.67 4.41 3.86
Q=0.6 0.0 0.0
0.8 0.0 0.0
8.6 0.0 0.0
enu =-.543 -.398 -.304
c =-.419 0.544 -.281
sqrdel=0.464 0.580 0.188
p =0.054 0.027 2.398
gamma =0.546 0.240 -.009
ATOM=Se P=4.95 4.84 4.17
Q=2.0 0.0 0.0
3.7 0.0 0.0
0.3 0.0 0.0
enu =-1.005 -0.388 -0.513
c =-1.304 -0.360 1.311
sqrdel= 0.344 0.387 0.596
p = 0.372 0.170 0.024
gamma = 0.442 0.145 0.150
ATOM=E P=1.5 2.5 3.5
Q=0 0 0
0 0 0
0 0 0
enu =-1.758 -0.642 1.316
c = 0.990 3.503 6.985
sqrdel= 0.590 0.485 0.400
p = 0.006 0.003 0.001
gamma = 0.358 0.065 0.022
CHARGE LMTODAT=T ELF=F ADDCOR=F
SPINDENS=F
CHARWIN=F EMIN=-2 EMAX=2
PLOT ORIGIN=0 0 0
R1=1 0 0 NDELR1=0
R2=0 1 0 NDELR2=0
R3=0 0 1 NDELR3=0
FORMAT=1
BZ NKABC=4 4 4 TETRA=T METAL=T
TOL=.000001
N=0 W=.005 RANGE=5 NPTS=1001
EWALD NKDMX=250 AS=2 TOL=.000001
RHOFIT FIT=F KAPPA2=0 RMAXS=3.5
ATOM=Ni LMXRHO=2 SIGMA=.7 .7 .7
ATOM=Se LMXRHO=2 SIGMA=.7 .7 .7
ATOM=E LMXRHO=2 SIGMA=.7 .7 .7
SCELL PLAT=1 0 0
0 1 0
0 0 1 EQUIV=T
HARTREE BEGATOM=T LT1=2 LT2=2 LT3=2
DOS NOPTS=801 EMIN=-2 EMAX=2
SYML NQ=30 Q1=0.0 0.0 0.0 LAB1=g
Q2=0.5 0.5 0.0 LAB2=M
NQ=20 Q1=0.5 0.5 0.0 LAB1=M
Q2=0.5 0.0 0.0 LAB2=X
NQ=20 Q1=0.5 0.0 0.0 LAB1=X
Q2=0.0 0.0 0.0 LAB2=g
NQ=35 Q1=0.0 0.0 0.0 LAB1=g
Q2=0.5 0.5 0.5 LAB2=R
FINDES RMINES=.9 RMAXES=4 NRXYZ=72 72 72
Notice that the Wigner-Sitz radii have been inserted because SCLWSR=T.
This is a complete CTRL file. The meaning of only a few of these tokens is necessary in order to run the program, however, a complete list with a description of each token is given in SectionV.