Input data is specified in an input file. The
system, Q_0 and normal mode vectors are contained in what is
termed the file0 file. Output is to a
set of point files , each containing a
separate geometry. Information needed to run the quantum
chemistry calculations can be specified using the opening and closing files . A go file is also created that can be used to launch
all the calculations.
or
vcpnt input
where where input (or input.inp) denotes the input file. The input format uses, like all the Quantics package input files, keywords that are for the most part free format and case insensitive. See Quantics input file structure
vcpnt input.inp
for further information on the general use of keywords, noting that there are no sections in the VCHAM input files. The input file ends with the keyword end-input
Defining the input data files | |||||||||||||||||
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Keyword | Description | ||||||||||||||||
file0 = S | S is name of file containing normal modes and Q0 geometry | ||||||||||||||||
nmodes = I (, I1) | System contains I normal modes and I1 trivial degrees of freedom (default 6). |
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all_eigenvectors | Use all Hessian eigenvectors, including those corresponding to translations and infinitesimal rotations. |
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fileout = S | S is the file stem for the point files containing the geometries | ||||||||||||||||
formout = S |
format for point files:
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file0orient = S | If the file0 is a Gaussian output file, by default the coordinates are taken from the Input orientation. If S=standard, the Standard orientation coordinates are taken. It is good practice, and less likely to cause errors, if the Input and Standard orientations are the same, i.e. the molecule is in the high symmetry orientation. |
Next the way the points are to be generated must be specified . A single keyword is required, and it must be alone on a line.
Defining the points | |
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Keyword | Description |
along = M I R | 2*I+1 points will be created along the Mth mode with an increment of R. |
along_all = I R | Cuts containing 2*I+1 points will be created along all modes with an increment of R. |
grid2d = M M1 I I1 R R1 | A 2D grid with 2*I+1 points along the M th mode with an increment of R, and 2*I1+1 points along the M1 th mode with an increment of R1 will be set up. |
grid3d = M M1 M2 I I1 I2 R R1 R2 | A 3D grid with 2*I+1 points along the M th mode with an increment of R, 2*I1+1 points along the M1 th mode with an increment of R1, and 2*I2+1 points along the M2 th mode with an increment of R2 will be set up. |
rotate = M I R | 2*I+1 points will be created along the Mth mode with an increment of R. The mode will be treated as a torsion. |
nm2curv dihed = M | transforms the normal mode M to the dihedral angle defined by the atoms in dihed-section (See note 1 below). |
diagonal = M M1 I R R1 | A diagonal cut with 2*I+1 points between the M th and M1 th modes will be set up. The increment along M will be R, and along M1, R1. |
vector_points = R [, R1] | Number of points generated along vector defined in a "define" or "vector_define" section. If R1 is specified, this number of points is added at either end of the cut. |
vector_points = R | Number of points generated along vector defined in vector_define section |
define i Q_i end-define |
A definite point in Q-space as a list of values (one to a line): Q_i is the value of the ith mode. Generates a cut to the point starting at Q=0. The point defined is at Q=10 (10R). |
vector_define initial Q_1 ... Q_f final Q_1 ... Q_f end-vector_define |
Q-space coordinates that define a vector Q(final) - Q(initial). Generates a cut along the vector starting at Q=0 ending at Q=10 (10R). |
noq0 | The equilibrium geometry point Q0 will not be created. |
set = I | The points to be created are set I of this type. By default set = 0. |
qval M val | Cut at normal mode M at the value val |
The program will
set up files containing the geometries of the points at which
quantum chemical information will be calculated. The exact file
names will combine the defined filestem with the mode and point
number. Thus if the filestem for the points file has been set
using fileout = points , and a cut along mode m is made
with P points either side of Q0 ( along = M , P , XX ,)
then 2P+1 files are created with names points_M_Pl,
points_M_(P-1)l,... points_M_000, points_M_1r, ...
points_M_Pr where l and r denote "left"
and "right" (i.e. minus and plus) wrt Q0.
Note 1: defining a dihedral
If the nm2curv dihedral keyword is used
the atoms to be kept fixed and those that are to be rotated are specified in the
dihed-section. Each atom is listed in the same order as in the file0, followed
by a letter denoting its place. In the digram below a,b and c are frozen and each of
the atoms labeled d are rotated.
The atom denoted a is not rotated but used as the reference for the dihedral angle. A is connected to b which forms part of the b-c bond which the dihedral angle is rotated about. The above digram would require the following example input section.
dihed-section
H a
O b
C c
H d
H d
H d
end-dihed-section
Any other atoms in the molecule which are not to be rotated and do not form part of the dihedral bond must be frozen using the flag f A full example using 1,1-Difluoroethylene is shown available here aswell as the file0 used for reference here.
Keyword | Description |
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opening = S | information in file S to be written to start of point files (before geometry). |
closing = S | information in file S to be written to end of point files (after geometry). |
Special strings in opening and closing files | |
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String | Substitued by |
$filestem$ | filestem of created point file |
Keyword | Description |
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go_none | The go.com file is not created. |
subcmd = S | The command S is used to submit a job to the local machine. The default is qsub |
go_add | An exisiting go.com file is not overwritten but new commands added. Thus if a number of cuts are to be generated a single go.com file can be generated to start all the calculations. |
go_cmd ... end-go_cmd |
The commands written between the two keywords are used to set up the go.com file. |
On running
vcpnt crco5_pnt.inp11 points are generated along the first vibrational mode at Q_1 = -2.5, -2, -1.5, ..., 2, 2.5 and stored in the files crco5_1_05l.com , crco5_1_04l.com ...., crco5_1_000.com, crco5_1_01r.com, crco5_1_02r.com ...., crco5_1_05r.com. The filenames contain the string specified by fileout, the mode (_1) and the point (_Nl to the negative side of Q0 and _Nr to the positive where N is an integer). The format of these files is suitable for a GAUSSIAN calculation. See how the information from the opening and closing files is incorporated. Notice also how the string $filestem$ in the opening file has been replaced by the correct name for the checkpoint file.
Now the electronic structure calculations can be run. The file go.com has been generated to do this. If a submission command other than qsub is required, this can be changed using the subcmd keyword in the input file. As the calculations specified require a checkpoint file (guess = read) these must be provided by copying the master checkpoint file at Q0 to the names required by the point files. Now type
go.comand wait for the results.