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grdvec.man
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AIMPAC Utilities grdvec(3)
NAME
grdvec - calculates gradient paths of a charge distribution
SYNOPSIS
grdvec vecfile wfnfile
DESCRIPTION
grdvec calculates gradient paths in the charge distribution
as requested by the user, outputting the calculated paths
into a file ready to be sent to the plotter. The vecfile
contains the number and type of gradient paths desired as
outlined below. The wfnfile contains the wavefunction for
the molecule in terms of basis functions calculated by one
of the ab initio molecular orbital packages. The gradient
paths are calculated and written to an output file for
redirection to the plotter.
ARGUMENTS
vecfile (for example 'c4h4.vec')
The vecfile, described below, describes the orientation
of the chosen plane, the number, and the types of origins
desired within that plane.
wfnfile (for example 'c4h4.wfn')
The wavefunction file contains the basis set and optimized
coefficients from a SCF calculation describing the charge
distribution of that molecule.
FORMAT
The input to GRDVEC 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: Tetrahedrane, bisecting plane atoms and interatomic surfaces
PLOT: 10.0 0.100
CENTR: 0.0 0.0 0.0
PARAM: 0.1 0.005 0.005 1.0E-12 0 1
PLANE: 0 1 2 5 6
NORIG: 10
9.71207959E-10 1.98184301E-09 1.15576886E+00 1 2 2
1.72948569E+00 1.72948569E+00 1.72948568E+00 1 2 2
-1.72948569E+00 -1.72948569E+00 1.72948568E+00 1 2 2
3.99523990E-01 3.99523987E-01 -3.99523978E-01 1 2 2
-3.99523982E-01 -3.99523994E-01 -3.99523989E-01 1 2 2
0.97775600 0.97775600 0.97775600 0 0 36
-0.97775600 -0.97775600 0.97775600 0 0 36
2.13806500 2.13806500 2.13806500 0 0 36
-2.13806500 -2.13806500 2.13806500 0 0 36
1.35374830E-09 -4.33080537E-09 -1.15576886E+00 0 0 36
The cards are used as follows:
TITLE: Tetrahedrane HF/6-31G*
The first card is a 60 character title card.
PLOT: 10.0 0.100
The second card defines the grid size and density. The first real
number (N1) is the length of either axis of the grid in atomic
units (all values are in atomic units). The second real number (N2)
is the distance between each grid point along the axis. This
defines the density of the grid as there will be N1/N2 points
along each axis and hence (N1/N2)**2 grid points in total. GRDVEC
uses this information for scaling of the plots only, not in
the determination of the gradient paths. It is a good and
suggested practice to use the same values for PLOT for
GRDVEC as used in GRID.
CENTR: 0.0 0.0 0.0
The third card defines the center of the plot in the molecular
frame of reference. The grid will be evenly placed about this
point.
PARAM: 0.1 0.005 0.005 1.0E-12 0 1
The PARAM line contains five parameters used in the walking
algorithm. The first number is the distance (in a.u., as are
the rest) from an attractor that the walk is started. The
second and third are the distances from the defined repellors
that the uphill and downhill walks are started, respectively.
The fourth number is the endpoint criterion for all walks. The
next number determines whether the gradient vector paths are
allowed out of the plane or not. A zero (0) means that the paths
are to remain in the plane and a one (1) allows the gradient
vectors to leave the plane of the atoms. The former is used
most often while the latter is used primarily for molecular
graphs. The last number is the slow/fast walking switch. A zero
(0) means walk slowly (carefully) and a one (1) means step
quickly. The fast switch should be set first and only turned
off if difficulty is encountered.
PLANE: 0 1 2 5 6
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, 5, and 6 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 tetrahedrane molecule were
such that the four atoms of interest were in the YZ plane in the
wavefunction file the following card would place those atoms in
the plotter's XY plane.
PLANE: 1 90.0 90.0 0.0
This corresponds to rotation about the Z axis, placing the atoms
in the XZ plane. The second rotation about the X axis places
the atoms in the XY plane. And the user has decided not to
reorient the plane now that it is in the XY plane, hence the
third angle is 0.0.
NORIG: 10
This card inputs the number of origins to be used. GRDVEC is
dimensioned to handle up to 60 origins. Following this card are
NORIG cards upon which are the origin coordinates and descriptors.
9.71207959E-10 1.98184301E-09 1.15576886E+00 1 2 2
1.72948569E+00 1.72948569E+00 1.72948568E+00 1 2 2
-1.72948569E+00 -1.72948569E+00 1.72948568E+00 1 2 2
3.99523990E-01 3.99523987E-01 -3.99523978E-01 1 2 2
-3.99523982E-01 -3.99523994E-01 -3.99523989E-01 1 2 2
0.97775600 0.97775600 0.97775600 0 0 36
-0.97775600 -0.97775600 0.97775600 0 0 36
2.13806500 2.13806500 2.13806500 0 0 36
-2.13806500 -2.13806500 2.13806500 0 0 36
1.35374830E-09 -4.33080537E-09 -1.15576886E+00 0 0 36
Each card lists the Cartesian coordinates of the origin followed
be three integers describing the type of origin and number of
ascending and descending gradient paths from that origin. A (2,-2)
origin in the plane is an attractor in that plane and is
described by a descriptor '0'. From each attractor there are
no ascending paths of grad rho, only descending. (e.g. from that
point paths of grad rho may only descend. Thus for the first
two cards in the example, each is an attractor in the chosen
plane and the user has requested that 36 descending gradient
paths be mapped from each one. The other critical point of
interest in a plane is the (2,0) (the (2,+2) paths are always
the end points of gradient paths and will always be found by
descending paths in grad rho from the other two types of critical
points.) and it is described by a descriptor of '1'. The user
has requested that 2 ascending and 2 descending gradient paths be
calculated from these points.
OUTPUT
GRDVEC generates an output file with the file extension '.gvp'
which contains the calculated gradient paths. This file
may be plotted by redirecting the output to the plotter.
On unix machines, the appropriate command would be:
$ cat c4h4.gvp > /dev/tty02 (printer device)
EXAMPLES
grdvec c4h4 c4h4
This requests the calculation of the gradient vector
paths from the origins as described in the file c4h4.vec
using the wavefunction in c4h4.wfn.
SEE ALSO
extreme(3), grid(3), contor(3), relief(3), cube(3), envelope(3)
Release 1.0 AIMPAC grdvec(3)