Center for Computational Chemistry.
MOLCRYST Quick Reference.
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* MOLCRYST *
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This program is to calculate the structural parameters of molecular
crystals in the framework of atom-atom potentials scheme and dynamics of
these crystals in the quasiharmonic approximation.
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TO RUN MOLCRYST YOU NEED CREATE FILE WITH NAME INPUT AND RUN
MOLCRYST.EXE. pROGRAM WILL GENERATE OUTPUT FILE WITH NAME OUTFILE.
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* INSTRUCTIONS FOR CREATING INPUT FILES *
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1. FIRST CARD
Title of the job.
*------------------------------------------------------------------------
2. SECOND CARD
Three periods and three angles in the primitive cell; every parameter
must be accompanied by the optimization flag: 0 - do not optimize
this parameter, 1 - to optimize it.
*------------------------------------------------------------------------
3. THIRD CARD
Number of molecules in the primitive cell.
*------------------------------------------------------------------------
4. FOURTH CARD
Number of types of molecules and number of symmetrically independent
molecules.
*------------------------------------------------------------------------
5. FIFTH CARD
Three numbers of cells for summation along every direction.
*------------------------------------------------------------------------
6. SIXTH CARD
The type of potential (0 - Buckingham, 1 - 6-12), number of points,
in which the phonon spectra must be calculated, number of
temperatures, for which the vibrational contribution to the
Helmgoltz energy must be calculated, number of directions, along
which the sound velocity in the crystal must be calculated.
*------------------------------------------------------------------------
7. SEVENTH CARD
For every point, in which the phonon spectrum must be calculated, its
coordinates in the reciprocal space and the flag of printing
eigenvectors of normal vibrations (0 - do not print, 1 - to print).
*------------------------------------------------------------------------
8. EIGTH CARD
For every temperature its value must be pointed. After these the
number of points N along every direction which defines the points of
scanning of the reciprocal space (their number is of N**3 order) must
be written in the individual string
*------------------------------------------------------------------------
9. NINTH CARD
Strings containing three coordinates defining the directions of sound
velocity to be calculated.
*------------------------------------------------------------------------
10. TENTH CARD
For every type of molecule the number of atoms. After this individual
strings containing for every atom in the molecule three cartesian
coordinates in the coordinate system associated with the molecule,
the ordinal number in the periodic system and the atomic mass.
*------------------------------------------------------------------------
11. ELEVENTH CARD
For every independent molecule in the primitive cell the type, three
angles of rotation and three shifts (in the fractions of periods),
defining the position of the centre of mass. After each parameter
(except for type) the optimization flag must be printed.
*------------------------------------------------------------------------
12. TWELFTH CARD
For every dependent molecule in the primitive cell the number of the
independent molecule, on which it symmetrically depends, the relation
between the angles of rotation of dependent and independent
molecules and the relative shift of dependent molecule, determining
the position of its center of mass.
*------------------------------------------------------------------------
13. THIRTEENTH CARD
The pressure.
*------------------------------------------------------------------------
===========================================================================
FIND A SAMPLE input FILE BELOW
===========================================================================
Naphtalin
7.96 0 5.96 0 8.62 0 90.0 0 123.5 0 90.0 0
2
1 2
1 1 1
1 1 0 0
0. 0. 0. 1
18
.0000 .6950 .0000 6 12.0000
1.2041 1.3899 .0000 6 12.0000
2.4080 .6948 .0000 6 12.0000
-1.2039 1.3900 .0000 6 12.0000
-2.4080 .6951 .0000 6 12.0000
.0000 -.6950 .0000 6 12.0000
1.2039 -1.3901 .0000 6 12.0000
2.4080 -.6952 .0000 6 12.0000
-1.2041 -1.3900 .0000 6 12.0000
-2.4080 -.6949 .0000 6 12.0000
1.2042 2.4699 .0000 1 1.0000
3.3431 1.2347 .0000 1 1.0000
-1.2038 2.4700 .0000 1 1.0000
-3.3429 1.2302 .0000 1 1.0000
1.2038 -2.4701 .0000 1 1.0000
3.3429 -1.2303 .0000 1 1.0000
-1.2042 -2.4700 .0000 1 1.0000
-3.3431 -1.2298 .0000 1 1.0000
1 64.92 0 -64.99 0 75.05 0 0.0 0 0.0 0 0.0 0
1 -64.55 0 114.87 0 74.68 0 0.5 0 0.5 0 0.0 0
0.0
=============================================================================
FIND A SAMPLE outfile FILE BELOW
=============================================================================
Naphtalin
T(1)= 7.96 T(2)= 5.96 T(3)= 8.62
ALF= 90.00 BET= 123.50 GAM= 90.00
NMUC= 2
TYPES OF MOLECULES 1 INDEPENDENT 2
INFORMATION ON ATOMS ENTERING THE MOLECULE OF THE 1-TH TYPE
X= .0000 Y= .6950 Z= .0000 ITA= 6 MASS= 12.0000
X= 1.2041 Y= 1.3899 Z= .0000 ITA= 6 MASS= 12.0000
X= 2.4080 Y= .6948 Z= .0000 ITA= 6 MASS= 12.0000
X= -1.2039 Y= 1.3900 Z= .0000 ITA= 6 MASS= 12.0000
X= -2.4080 Y= .6951 Z= .0000 ITA= 6 MASS= 12.0000
X= .0000 Y= -.6950 Z= .0000 ITA= 6 MASS= 12.0000
X= 1.2039 Y= -1.3901 Z= .0000 ITA= 6 MASS= 12.0000
X= 2.4080 Y= -.6952 Z= .0000 ITA= 6 MASS= 12.0000
X= -1.2041 Y= -1.3900 Z= .0000 ITA= 6 MASS= 12.0000
X= -2.4080 Y= -.6949 Z= .0000 ITA= 6 MASS= 12.0000
X= 1.2042 Y= 2.4699 Z= .0000 ITA= 1 MASS= 1.0000
X= 3.3431 Y= 1.2347 Z= .0000 ITA= 1 MASS= 1.0000
X= -1.2038 Y= 2.4700 Z= .0000 ITA= 1 MASS= 1.0000
X= -3.3429 Y= 1.2302 Z= .0000 ITA= 1 MASS= 1.0000
X= 1.2038 Y= -2.4701 Z= .0000 ITA= 1 MASS= 1.0000
X= 3.3429 Y= -1.2303 Z= .0000 ITA= 1 MASS= 1.0000
X= -1.2042 Y= -2.4700 Z= .0000 ITA= 1 MASS= 1.0000
X= -3.3431 Y= -1.2298 Z= .0000 ITA= 1 MASS= 1.0000
MOLECULE TYPE: 1
ROT(1)= 64.92 ROT(2)= -64.99 ROT(3)= 75.05
TOP(1)= .000 TOP(2)= .000 TOP(3)= .000
MOLECULE TYPE: 1
ROT(1)= -64.55 ROT(2)= 114.87 ROT(3)= 74.68
TOP(1)= .500 TOP(2)= .500 TOP(3)= .000
OPTIMIZED VARIABLES - 0
PRESSURE = .0KBAR
FX= -22.877993237635620 KCAL/MOL
SPECTRUM IN POINT .0000, .0000, .0000 (CM-1)
U V W
122.4663 .8385 .5443 -.0235
61.6430 -.5232 .8165 .2441
70.3926 .1520 -.1924 .9695
U V W
123.8216 .7923 -.6101 -.0023
96.4197 .5910 .7685 -.2452
73.0763 .1514 .1929 .9695
a b c
103.6802 .9981 .0026 .0615
58.7137 -.0028 1.0000 .0045
46.8609 -.0615 -.0047 .9981
a b c
.0000 .9981 .0026 .0615
.0000 -.0028 1.0000 .0045
.0000 -.0615 -.0047 .9981
OPTIMAL LATTICE PARAMETERS
T(1)= 7.96 T(2)= 5.96 T(3)= 8.62
ALF= 90.00 BET= 123.50 GAM= 90.00
RDT(1)= 64.92 RDT(2)= -64.99 RDT(3)= 75.05
RDT(1)= -64.55 RDT(2)= 114.87 RDT(3)= 74.68
ENERGY= -.4576D+02
UCELL= -5.49
NM= 1 NA= 1
X= -.28 Y= .63 Z= -.10
NM= 1 NA= 2
X= -.44 Y= 1.49 Z= .98
NM= 1 NA= 3
X= -.02 Y= 1.10 Z= 2.25
NM= 1 NA= 4
X= -.70 Y= 1.02 Z= -1.36
NM= 1 NA= 5
X= -.55 Y= .15 Z= -2.44
NM= 1 NA= 6
X= .28 Y= -.63 Z= .10
NM= 1 NA= 7
X= .70 Y= -1.02 Z= 1.36
NM= 1 NA= 8
X= .55 Y= -.15 Z= 2.44
NM= 1 NA= 9
X= .44 Y= -1.49 Z= -.98
NM= 1 NA=10
X= .02 Y= -1.10 Z= -2.25
NM= 1 NA=11
X= -.88 Y= 2.47 Z= .83
NM= 1 NA=12
X= -.14 Y= 1.78 Z= 3.09
NM= 1 NA=13
X= -1.14 Y= 1.99 Z= -1.51
NM= 1 NA=14
X= -.87 Y= .45 Z= -3.43
NM= 1 NA=15
X= 1.14 Y= -1.99 Z= 1.51
NM= 1 NA=16
X= .87 Y= -.45 Z= 3.43
NM= 1 NA=17
X= .88 Y= -2.47 Z= -.83
NM= 1 NA=18
X= .14 Y= -1.77 Z= -3.09
NM= 2 NA= 1
X= 3.60 Y= 3.61 Z= -2.10
NM= 2 NA= 2
X= 3.75 Y= 4.47 Z= -3.18
NM= 2 NA= 3
X= 3.33 Y= 4.08 Z= -4.45
NM= 2 NA= 4
X= 4.02 Y= 4.00 Z= -.83
NM= 2 NA= 5
X= 3.87 Y= 3.13 Z= .24
NM= 2 NA= 6
X= 3.04 Y= 2.35 Z= -2.29
NM= 2 NA= 7
X= 2.62 Y= 1.96 Z= -3.56
NM= 2 NA= 8
X= 2.77 Y= 2.83 Z= -4.64
NM= 2 NA= 9
X= 2.89 Y= 1.49 Z= -1.22
NM= 2 NA=10
X= 3.30 Y= 1.88 Z= .05
NM= 2 NA=11
X= 4.19 Y= 5.45 Z= -3.03
NM= 2 NA=12
X= 3.45 Y= 4.76 Z= -5.28
NM= 2 NA=13
X= 4.45 Y= 4.97 Z= -.68
NM= 2 NA=14
X= 4.19 Y= 3.43 Z= 1.23
NM= 2 NA=15
X= 2.18 Y= .99 Z= -3.71
NM= 2 NA=16
X= 2.45 Y= 2.53 Z= -5.62
NM= 2 NA=17
X= 2.45 Y= .51 Z= -1.36
NM= 2 NA=18
X= 3.19 Y= 1.21 Z= .89