diff --git a/1.html b/1.html index 362c991..cbceaac 100644 --- a/1.html +++ b/1.html @@ -418,8 +418,7 @@

History#<

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) time.

diff --git a/2.html b/2.html index dbc9670..47ce58f 100644 --- a/2.html +++ b/2.html @@ -488,7 +488,7 @@

Input Browsing Data Files#

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 several optional keyword values available, however, only one option is @@ -497,13 +497,16 @@

Keyword input@DATAFILETYPE keyword#

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 stored.

@@ -513,20 +516,20 @@

@DATAFILETY

@DATAFILEPATH keyword#

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.

@ENERGY keyword#

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.

GeomOnly: Only calculate the value of these internal coordinates.

@@ -536,7 +539,7 @@

@PARM

@VIBRATION keyword#

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.

@@ -545,7 +548,7 @@

@DIRCURVThis 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.

@@ -553,7 +556,7 @@

@DIRCURV@AVAM keyword#

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 must be set to on and the @DIRCURV must be set to on

@@ -562,7 +565,7 @@

@AVAM@CURVCPL keyword#

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 @DIRCURV must be set to on.

@@ -571,7 +574,7 @@

@CURVCPL@CORIOLIS keyword#

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.

@@ -579,7 +582,7 @@

@CORIOLIS@ADIABFC keyword#

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.

@@ -588,19 +591,23 @@

@ADIABFCSection input#

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.

@@ -613,53 +620,57 @@

PARAMETER -

\ ``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#

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#

@@ -670,12 +681,14 @@

AUTOSMTH

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#

@@ -689,11 +702,13 @@

RMSPK

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#

@@ -730,18 +745,20 @@

DMO\(N_{left}\)( 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
+
+

diff --git a/_sources/1.md b/_sources/1.md index 6315c8e..de92a2c 100644 --- a/_sources/1.md +++ b/_sources/1.md @@ -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) diff --git a/_sources/2.md b/_sources/2.md index d1f8a6d..ea841d7 100644 --- a/_sources/2.md +++ b/_sources/2.md @@ -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. @@ -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. @@ -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 @@ -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 @@ -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. @@ -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. @@ -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`. @@ -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`. @@ -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` @@ -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 @@ -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`. @@ -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`. @@ -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. @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 +``` diff --git a/searchindex.js b/searchindex.js index 29f0968..8ec823f 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"@ADIABFC keyword": [[1, "adiabfc-keyword"]], "@AVAM keyword": [[1, "avam-keyword"]], "@CORIOLIS keyword": [[1, "coriolis-keyword"]], "@CURVCPL keyword": [[1, "curvcpl-keyword"]], "@DATAFILEPATH keyword": [[1, "datafilepath-keyword"]], "@DATAFILETYPE keyword": [[1, "datafiletype-keyword"]], "@DIRCURV keyword": [[1, "dircurv-keyword"]], "@ENERGY keyword": [[1, "energy-keyword"]], "@PARM keyword": [[1, "parm-keyword"]], "@VIBRATION keyword": [[1, "vibration-keyword"]], "AUTOSMTH section": [[1, "autosmth-section"]], "Abbreviations": [[4, null]], "Adiabatic force constant": [[2, "adiabatic-force-constant"]], "Before we start": [[0, null]], "CURVCOR section": [[1, "curvcor-section"]], "DMO section": [[1, "dmo-section"]], "Decomposition of reaction path direction and curvature into internal coordinates": [[2, "decomposition-of-reaction-path-direction-and-curvature-into-internal-coordinates"]], "Energy and derivatives": [[2, "energy-and-derivatives"]], "Example 1. HCN \\rightarrow HNC isomerization": [[3, "example-1-hcn-rightarrow-hnc-isomerization"]], "Example 2. CH_3 + H_2 \\rightarrow CH_4 + H": [[3, "example-2-ch-3-h-2-rightarrow-ch-4-h"]], "Example 3. 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