-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathcubev.man
125 lines (96 loc) · 5.19 KB
/
cubev.man
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
AIMPAC Utilities cube(3)
NAME
CUBEV - calculates cube of properties (in atomic units).
SYNOPSIS
cubev infile wfnfile
DESCRIPTION
This is a vectorized version of old CUBE program.
The cubev program reads the input data from the infile
and the wavefuction from the wfnfile and calculates
a cube of values of the requested property.
ARGUMENTS
infile (for example 'hcoh.inf')
The input file describes the type and characteristics of the
desired calculation.
wfnfile (for example 'hcoh.wfn')
The wavefunciton file contains the basis set and optimized
coefficients from a SCF calculation describing the charge
distribution of that molecule.
FORMAT
The input to CUBEV is free format with the first seven characters
of each card being ignored by the routine and used by the user
as labels for ease of use. An example of the input is given here.
TITLE: Formaldehyde HF/3-21G//HF/3-21G rho
INCRM: 10.0 0.100 0
CENTR: 0.0 0.0 0.0
PLANE: 0 1 2 3 4
NFUNC: 1
The cards are used as follows:
TITLE: Formaldehyde HF/3-21G//HF/3-21G rho
The first card is a 60 character title card.
INCRM: 10.0 0.100 0
The second card defines the cube size and density. The first real
number (N1) is the length of the axis of the cube in atomic
units (all values are in atomic units). The second real number (N2)
is the distance between each cube point along each axis. This
defines the density of the cube as there will be N1/N2 points
along each axis and hence (N1/N2)**3 cube points in total. CUBE
is dimensioned to handle up to a 200 X 200 X 200 cube.
The third (integer) number alows the user to take advantage of
molecular symmetry which will speed up the calculation of the cube.
A value of 0 means the cube will be calculated by not taking advantage
of symmetry. A value of 1 means there is symmetry in Y. A value
of 2 means there is symmetry in both X and Y.
CENTR: 0.0 0.0 0.0
The third card defines the center of the plot in the molecular
frame of reference. The cube will be evenly placed about this
point.
PLANE: 0 1 2 3 4
The fourth card allows the user to define the plane of interest
for this calculation rotating it to the XY plane of the plotter.
The user has a choice of two methods for description of the plane,
inertial axis or Euler angles. The first integer read determines
which method is used. If the integer value is zero inertial axis
is to be used. The integers following are the atom numbers of
those atoms within the plane. Any number of atoms (up to 30) may
be used to define the plane (three atoms define a plane, but more
may be entered). In this case, the user has requested that atoms
1, 2, 3, and 4 be placed in the plane. If the atoms do not define
a plane, the routine will make a best fit to the plane and the
results will most likely not be desirable. If the integer value
is 1 then Euler angles will be used. The first real number is
the rotation, in degrees, about the molecular Z axis. (Positive
rotations correspond to clockwise rotations when viewing down
that axis toward the origin from the positive axis) The second
real number is the rotation about the molecular X axis. The third
is the rotation about the Z axis of the plotter's frame. For
example if the formaldehyde molecule were in the YZ plane in
the wavefunction file the following card would place the molecule
in the plotter's XY plane.
PLANE: 1 90.0 90.0 0.0
This corresponds to rotation about the Z axis, placing the molecule
in the XZ plane. The second rotation about the X axis places
the molecule in the XY plane. And the user has decided not to
reorient the molecule now that it is in the XY plane, hence the
third angle is 0.0.
This feature is merely a carry-over from the GRID routine and is
not terribly usefull here. It is suggested that the initial cube
runs use the following card;
PLANE: 0
which performs no orientation manipulation on the cube.
NFUNC: 1
The last card chooses the function to be calculated at each point
in the cube. An integer value of 1 chooses rho while a value of
2 chooses del-squared rho. Other functions are presently being
implemented and will follow in later releases.
OUTPUT
CUBEV generates a file containing the requested cube of data.
This file will have the file extension '.qub'. The cube may
be processed by running it through envelope.
EXAMPLES
cubev hcoh hcoh
This requests a calculation of the cube described in hcoh.inf
using the wavefuction in hcoh.wfn.
SEE ALSO
envelope(3), grid(3), contor(3), relief(3)
Release 1.0 AIMPAC cube(3)