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2024 #5

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Sep 11, 2024
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9c9dbbe
Formating fixes.
rkalescky Sep 11, 2024
ee7cea7
Updated for Python3.
rkalescky Sep 11, 2024
285e7ff
Updated authors.
rkalescky Sep 11, 2024
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3 changes: 1 addition & 2 deletions docs/1.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,7 @@ version of the URVA program was then named as **URVA**.

## Execution of URVA

The proper execution of URVA requires Python interpreter with the
version 2.7.x. Versions lower than this might lead to trouble.
The proper execution of URVA requires modern Python3 interpreter.

Here are the list of Python modules needed to run URVA: (1) NumPy, (2)
SciPy, (3) SymPy, (4) sys, (5) os, (6) copy, (7) gc, (8) math and (9)
Expand Down
179 changes: 85 additions & 94 deletions docs/2.md
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Expand Up @@ -29,6 +29,10 @@ implementation.\]

An old version of browsing file `IRC.forward` looks like this:

```{include} data/IRC.forward
:literal:
```

This is all browsing information for one point along the reaction path,
a complete browsing file contains many points.

Expand Down Expand Up @@ -57,6 +61,10 @@ coordinate(parameter).

A new version of browsing file `for.urv` looks like this:

```{include} data/for.urv
:literal:
```

To distinguish from old browsing file, the first line is
`BEGIN (no Hessian)`, indicating that this browsing file does not
contains Hessian information and is a new browsing file.
Expand Down Expand Up @@ -90,7 +98,7 @@ floating number.
Just for convenience, keyword input is often written before section
input. The format of keyword input line is:

`@``keyword_name``=``[keyword_value]`
`@keyword_name = [keyword_value]`

The `@` symbol should be in the first column. No space is allowed
after it. On both sides of = sign, it should be space. There might be
Expand All @@ -102,15 +110,16 @@ accepted.
This keywords specifies the format of input data source file for URVA
analysis.

`@DATAFILETYPE``=``old/new/xyz`
`@DATAFILETYPE = old/new/xyz`

`old`: The input data source file is generated by Gaussian package by
setting corresponding IOp(1/45). This type of data contains most
complete information.

*NOTE: If the data file is generated by Gaussian with version number
```{note} If the data file is generated by Gaussian with version number
lower than 16.A, all floating numbers should be converted from "D" into
"E" format.*
"E" format.
```

`new`: The input data source file is generated by a modified version
of Gaussian package. This type of data has no Hessian and gradient
Expand All @@ -123,7 +132,7 @@ snapshots.

This keyword specifies the path of the input data file.

`@DATAFILEPATH``=``"../path/to/data/file"`
`@DATAFILEPATH = "../path/to/data/file"`

The quotation marks should be included.

Expand All @@ -132,14 +141,14 @@ The quotation marks should be included.
This keyword specifies whether SCF energy and its first and second
derivatives will be calculated.

`@ENERGY``=``on/off`
`@ENERGY = on/off`

### `@PARM` keyword

This keyword specifies the way to deal with internal coordinates
parameters provided by user.

`@PARM``=``No/GeomOnly/All`
`@PARM = No/GeomOnly/All`

`No`: Do nothing with regard to these internal coordinates
specifications.
Expand All @@ -153,7 +162,7 @@ related to these internal coordinates will be calculated.

This keyword specifies whether or not to do normal mode analysis.

`@VIBRATION``=``on/off`
`@VIBRATION = on/off`

If the keyword value is set to `on`, the `@DATAFILETYPE` must be set
to `old`.
Expand All @@ -164,7 +173,7 @@ This keyword decides whether or not to calculate reaction path direction
$\boldsymbol {\eta(s)}$ and curvature
$\boldsymbol {\kappa(s)}$.

`@DIRCURV``=``on/off`
`@DIRCURV = on/off`

If the keyword value is set to `on`, the `@DATAFILETYPE` must be set
to `old` or `new`.
Expand All @@ -174,7 +183,7 @@ to `old` or `new`.
This keyword specifies whether or not to calculate the adiabatic mode
coupling coefficient $\boldsymbol{ A_{n,s}(s)}$.

`@AVAM``=``on/off`
`@AVAM = on/off`

If the keyword value is set to `on`, the `@DATAFILETYPE` must be set
to `old`, the `@PARM` must be set to `All`, the `@VIBRATION`
Expand All @@ -185,7 +194,7 @@ must be set to `on` and the `@DIRCURV` must be set to `on`
This keyword specifies whether or not to calculate the curvature
coupling coefficient $\boldsymbol{B_{\mu,s}(s)}$.

`@CURVCPL``=``on/off`
`@CURVCPL = on/off`

If the keyword value is set to `on`, the `@DATAFILETYPE` must be set
to `old`, the `@VIBRATION` must be set to `on`, and the
Expand All @@ -196,7 +205,7 @@ to `old`, the `@VIBRATION` must be set to `on`, and the
This keyword specifies whether or not to calculate the Coriolis
mode-mode coupling coefficient $\boldsymbol{B_{\mu,\nu}(s)}$.

`@CORIOLIS``=``on/off`
`@CORIOLIS = on/off`

If the keyword value is set to `on`, the `@DATAFILETYPE` must be set
to `old` and the `@VIBRATION` must be set to `on`.
Expand All @@ -206,7 +215,7 @@ to `old` and the `@VIBRATION` must be set to `on`.
This keyword specifies whether or not to calculate adiabatic force
constant $\mathbf{k^a}$.

`@ADIABFC``=``on/off`
`@ADIABFC = on/off`

If the keyword value is set to `on`, the `@DATAFILETYPE` must be set
to `old` and the `@PARM` must be set to `All`.
Expand All @@ -216,28 +225,25 @@ to `old` and the `@PARM` must be set to `All`.
Section input is used when multiple parameters need to be read in, the
format of the section input is:

``` \ ``SECTION_NAME ```

``` \ ``parameter line_1 ```

``` \ ``parameter line_2 ```

``` \ ``... ```

``` \ ``END SECTION_NAME ```
```
SECTION_NAME
parameter line_1
parameter line_2
...
END SECTION_NAME
```

### `TITLE` section

This section accepts remarks provided by user. The content will be
displayed in standard output.

``` \ ``TITLE ```

``` \ ``Please put remarks here. ```

``` \ ``Multiple lines are accepted. ```

``` \ ``END TITLE ```
```
TITLE
Please put remarks here.
Multiple lines are accepted.
END TITLE
```

This section is quite useful to take note of the parameters we use for
URVA calculations.
Expand All @@ -253,65 +259,65 @@ pyramidalization angle, ring puckering amplitude, ring puckering phase
angle, ring deformation amplitude and ring deformation phase angle are
supported.

``` \ ``PARAMETER ```

``` \ ``Internal coordinate specification ```

``` \ ``END PARAMETER ```
```
PARAMETER
Internal coordinate specification
END PARAMETER
```

Bond length:

``` \ ``std ```$N_1$``` \ :math:`N_2`\ ``: "bond_name" ```
`std N_1 N_2 : "bond_name"

Bond angle:

``` \ ``std ```$N_1$``` \ :math:`N_2`\ `` ```$N_3$`: "angle_name"`
`std N_1 N_2 N_3: "angle_name"`

Dihedral angle:

``` \ ``std ```$N_1$``` \ :math:`N_2`\ `` ```$N_3$``` \ :math:`N_4`\ ``: "dihedral_name" ```
`std N_1 N_2 N_3 N_4 : "dihedral_name" `

Out of plane angle(the angle between the bond length
$N_1$-$N_2$ and the plane
$N_2$-$N_3$-$N_4$):

``` \ ``oop ```$N_1$``` \ :math:`N_2`\ `` ```$N_3$``` \ :math:`N_4`\ ``: "out_of_plane_name" ```
`oop N_1 N_2 N_3 N_4 : "out_of_plane_name" `

Pyramidalization angle(the angle $\theta_P$ is related to the
three bond angles $N_2$-$N_1$-$N_3$,
$N_3$-$N_1$-$N_4$,
$N_4$-$N_1$-$N_2$):

``` \ ``pyr ```$N_1$``` \ :math:`N_2`\ `` ```$N_3$``` \ :math:`N_4`\ ``: "pyramidalization_angle_name" ```
`pyr N_1 N_2 N_3 N_4 : "pyramidalization_angle_name" `

Radius of planar reference ring($R$)($N_{ring}$: number of
ring atoms):

``` \ ``ring ```$N_{ring}$`- (`$N_1$``` \ :math:`N_2`\ ``... ```$N_{atoms}$`) -[0 0]: "ring_breathing_name"`
`ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[0 0]: "ring_breathing_name"`

Planar deformation
amplitude($t_n$)(n=1$\sim$$N_{ring}-2$):

``` \ ``ring ```$N_{ring}$`- (`$N_1$``` \ :math:`N_2`\ ``... ```$N_{atoms}$`) -[1 n]: "deformation_amplitude_name"`
`ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[1 n]: "deformation_amplitude_name"`

Planar deformation phase
angle($\tau_n$)(n=1$\sim$$N_{ring}-2$):

``` \ ``ring ```$N_{ring}$`- (`$N_1$``` \ :math:`N_2`\ ``... ```$N_{atoms}$`) -[2 n]: "deformation_phase_angle_name"`
`ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[2 n]: "deformation_phase_angle_name"`

Puckering
amplitude($q_n$)(n=2$\sim$($N_{ring}-1$)/2 for odd
$N_{ring}$ or 2$\sim$$N_{ring}$/2 for even
$N_{ring}$):

``` \ ``ring ```$N_{ring}$`- (`$N_1$``` \ :math:`N_2`\ ``... ```$N_{atoms}$`) -[3 n]: "puckering_amplitude_name"`
`ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[3 n]: "puckering_amplitude_name"`

Puckering phase
angle($\phi_n$)(n=2$\sim$($N_{ring}-1$)/2 for odd
$N_{ring}$ or 2$\sim$$N_{ring}$/2-1 for even
$N_{ring}$):

``` \ ``ring ```$N_{ring}$`- (`$N_1$``` \ :math:`N_2`\ ``... ```$N_{atoms}$`) -[4 n]: "puckering_phase_angle_name"`
`ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[4 n]: "puckering_phase_angle_name"`

### `CURVCOR` section

Expand All @@ -320,13 +326,12 @@ The CURVCOR interface will be activated if this section is found.
For most situations, it is usually enough for $N_l$ and
$N_r$ to take the value of 25.

``` \ ``CURVCOR ```

``` \ ``Ln = ```$N_l$

``` \ ``Rn = ```$N_r$

``` \ ``END CURVCOR ```
```
CURVCOR
Ln = $N_l$
Rn = $N_r$
END CURVCOR
```

### `AUTOSMTH` section

Expand All @@ -342,17 +347,14 @@ Using the value of 3 is usually enough for $N_l$ and $N_r$.
$t$ is a cut-off for second derivative of smoothened curve.
Increase it when necessary. Recommended value: 2.5.

``` \ ``AUTOSMTH ```

``` \ ``StepSize = ```$\delta s$

``` \ ``Ln = ```$N_l$

``` \ ``Rn = ```$N_r$

``` \ ``d2ythresh = ```$t$

``` \ ``END AUTOSMTH ```
```
AUTOSMTH
StepSize = $\delta s$
Ln = $N_l$
Rn = $N_r$
d2ythresh = $t$
END AUTOSMTH
```

### `RMSPK` section

Expand All @@ -371,15 +373,13 @@ of $p$ will be labeled as spike condidates. Recommened value:
Gradient check threshold $g$ is used to filter out normal points
from spike candidates. Recommended value: 1.2.

``` \ ``RMSPK ```

``` \ ``CutHigh = ```$k$

``` \ ``Percentage = ```$p$

``` \ ``GradRatio = ```$g$

``` \ ``END RMSPK ```
```
RMSPK
CutHigh = $k$
Percentage = $p$
GradRatio = $g$
END RMSPK
```

### `DMO` section

Expand Down Expand Up @@ -421,26 +421,17 @@ one point off the TS point in reverse(or forward) direction also needs
to be skipped, $N_{left}$( or $N_{right}$) should be set
to 1.

``` \ ``DMO ```

``` \ ``Sthresh = ```$s_{max}$

``` \ ``Slowest = ```$s_{min}$

``` \ ``Np = ```$N_{min}$

``` \ ``NMax = ```$N_{max}$

``` \ ``Cut = ```$IO_{cut}$

``` \ ``CutA = ```$s_{start}$

``` \ ``CutB = ```$s_{end}$

``` \ ``Skip = ```$IO_{skip}$

``` \ ``SkipA = ```$N_{left}$

``` \ ``SkipB = ```$N_{right}$

``` \ ``END DMO ```
```
DMO
Sthresh = $s_{max}$
Slowest = $s_{min}$
Np = $N_{min}$
NMax = $N_{max}$
Cut = $IO_{cut}$
CutA = $s_{start}$
CutB = $s_{end}$
Skip = $IO_{skip}$
SkipA = $N_{left}$
SkipB = $N_{right}$
END DMO
```
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